% vtools show -h
usage: vtools show [-h] [-l N] [-v {0,1,2,3}]
[{project,tables,table,samples,phenotypes,genotypes,fields,annotations,annotation,track,formats,format,tests,test,runtime_options,runtime_option,snapshot,snapshots}]
[items [items ...]]
Output information of all system and project related items such as variant
tables, samples, phenotypes, annotation databases and fields.
positional arguments:
{project,tables,table,samples,phenotypes,genotypes,fields,annotations,annotation,track,formats,format,tests,test,runtime_options,runtime_option,snapshot,snapshots}
Type of information to display, which can be 'project'
for summary of a project, 'tables' for all variant
tables (or all tables if --verbosity=2), 'table TBL'
for details of a specific table TBL, 'samples [COND]'
for sample name, files from which samples are
imported, and associated phenotypes (can be supressed
by option --verbosity 0) of all or selected samples,
'phenotypes [P1 P2...]' for all or specified
phenotypes of samples, 'fields' for fields from
variant tables and all used annotation databases,
'annotations' for a list of all available annotation
databases, 'annotation ANN' for details about
annotation database ANN, 'track' for information of a
track file in tabixed vcf, bigWig, or bigBed format,
'formats' for all supported import and export formats,
'format FMT' for details of format FMT, 'tests' for a
list of all association tests, and 'test TST' for
details of an association test TST, 'runtime_options'
for a list of runtime options and their descriptions,
'runtime_option OPT' for value of specified runtime
option OPT, 'snapshot' for a particular snapshot by
name or filename, 'snapshots' for a list of publicly
available snapshots, and snapshots of the current
project saved by command 'vtools admin
--save_snapshots'. The default parameter of this
command is 'project'.
items Items to display, which can be, for example, name of
table for type 'table', conditions to select samples
for type 'samples', a list of phenotypes for type
'phenotypes', name of an annotation database for type
'annotation', a pattern to selected annotation
databases for type 'annotations', name of a format for
type 'format', and name of an association test for
type 'test'.
optional arguments:
-h, --help show this help message and exit
-l N, --limit N Limit output to the first N records.
-v {0,1,2,3}, --verbosity {0,1,2,3}
Output error and warning (0), info (1), debug (2) and
trace (3) information to standard output (default to
1).
Command `vtools show displays various project and system information. It accepts type of item to display as its first parameter, followed by names of items if information about particular items are needed. Generally speaking:
tables, tests) lists all available items. Options are usually available to limit the items to display.table, test) list details of a single item.-v0 can usually be used to suppress description of items, and -v2 can be used to show more information.project)Command `vtools show without parameter and `vtools show project displays general information about a project, including project name, reference genome, existing variant tables, and used annotation databases.
Let us load a fairly large project from an online snapshot vt_ExomeAssociation,
% vtools init show
% vtools admin --load_snapshot vt_ExomeAssociation
Downloading snapshot vt_ExomeAssociation.tar.gz from online
INFO: Load genotypes
INFO: Snapshot vt_ExomeAssociation has been loaded
% vtools show
Project name: show
Primary reference genome: hg19
Secondary reference genome: None
Runtime options: verbosity=1
Variant tables: rare
variant
Annotation databases:
The project has 2 variant tables, the master variant table and another variant tables rare. It uses the hg19 reference genome, and has not been connected to any annotation database.
tables and table)Command vtools show tables lists all variant tables, their creation dates and comments (if available). This command does not accept any additional parameter.
% vtools show tables
table #variants date message
rare 19,785 Jan24 rare variants
variant 26,797
vtools show tables lists all variant tables of a project, with creation date and comment. If you only need to know information about a particular variant table, it is easier and faster to use command vtools show table TABLE. This command lists date of creation, a short description, number of variants and fields (only the master variant table has multiple fields). Perhaps more interestingly, it shows the command that has been used to create this variant table, which usually contain import information regarding from which table this table is drawn, and what criteria has been used.
% vtools show table rare
Name: rare
Type: variant
Description: rare variants
Creation date: Jan24
Command: vtools select variant 'af<0.01 OR af>0.99' -t rare
'rare variants'
Fields: variant_id
Number of variants: 19785
samples)Command vtools show samples lists samples, files from which samples are imported, and phenotypes associated with each samples. The command by default lists all samples and phenotypes, but you can list part of the information by
--limit limit the output to the first few records--samples can limit the samples to those that match specified criteria-v 0 (--verbosity 0) supress phenotypes. This is useful when there are a large number of phenotypes-v 2 lists full filenames. The default output lists part of the filenames if they are too long. Increasing verbosity level will show complete information.% vtools show samples -l 10
sample_name filename gender age bmi status exposure
SAMP10 assoctest.dat 1 44 27.93818994 0 0
SAMP100 assoctest.dat 1 47 33.47268746 0 0
SAMP1000 assoctest.dat 1 50 26.4845 0 0
SAMP1001 assoctest.dat 2 59 24.02405 0 1
SAMP1002 assoctest.dat 2 61 26.32636 0 0
SAMP1003 assoctest.dat 1 49 24.4131 0 1
SAMP1004 assoctest.dat 1 57 30.57549 0 0
SAMP1005 assoctest.dat 2 57 28.40909 0 1
SAMP1006 assoctest.dat 2 48 28.7642 0 0
SAMP1007 assoctest.dat 1 65 24.14179 0 0
(3170 records omitted)
Show only male samples using condition gender=1 to select samples
% vtools show samples 'gender=1' -l 10
sample_name filename gender age bmi status exposure
SAMP10 assoctest.dat 1 44 27.93818994 0 0
SAMP100 assoctest.dat 1 47 33.47268746 0 0
SAMP1000 assoctest.dat 1 50 26.4845 0 0
SAMP1003 assoctest.dat 1 49 24.4131 0 1
SAMP1004 assoctest.dat 1 57 30.57549 0 0
SAMP1007 assoctest.dat 1 65 24.14179 0 0
SAMP1008 assoctest.dat 1 48 28.20037 0 1
SAMP1010 assoctest.dat 1 56 23.67424 0 1
SAMP1014 assoctest.dat 1 47 23.54056 0 0
SAMP1016 assoctest.dat 1 60 23.8961 0 0
(3170 records omitted)
Suppressing phenotypes and only show basic sample information
% vtools show samples -l 10 -v0
sample_name filename
SAMP10 assoctest.dat
SAMP100 assoctest.dat
SAMP1000 assoctest.dat
SAMP1001 assoctest.dat
SAMP1002 assoctest.dat
SAMP1003 assoctest.dat
SAMP1004 assoctest.dat
SAMP1005 assoctest.dat
SAMP1006 assoctest.dat
SAMP1007 assoctest.dat
(3170 records omitted)
phenotypes)Command vtools show phenotypes is similar to vtools show samples but it does not show filename information and can display only specified phenotypes.
% vtools show phenotypes -l 10
sample_name gender age bmi status exposure
SAMP10 1 44 27.93818994 0 0
SAMP100 1 47 33.47268746 0 0
SAMP1000 1 50 26.4845 0 0
SAMP1001 2 59 24.02405 0 1
SAMP1002 2 61 26.32636 0 0
SAMP1003 1 49 24.4131 0 1
SAMP1004 1 57 30.57549 0 0
SAMP1005 2 57 28.40909 0 1
SAMP1006 2 48 28.7642 0 0
SAMP1007 1 65 24.14179 0 0
(3170 records omitted)
Show values of specified phenotypes
% vtools show phenotypes exposure -l 10
sample_name exposure
SAMP10 0
SAMP100 0
SAMP1000 0
SAMP1001 1
SAMP1002 0
SAMP1003 1
SAMP1004 0
SAMP1005 1
SAMP1006 0
SAMP1007 0
(3170 records omitted)
Another command vtools phenotype --output can also output selected phenotypes. It is more powerful in that it has better control of the format of output, and more importantly, allow output of summary statistics of phenotypes.
genotypes)Command vtools show genotypes shows the number of genotypes and names of genotype info fields of each sample. Such information are useful for the calculation of summary statistics of genotypes (e.g. depth of coverage) using commands vtools phenotype –from_stat(statistics for each sample) andvtools update –from_stat@@ (statistics for each variant).
% vtools show genotypes -l 10
sample_name filename num_genotypes sample_genotype_fields
SAMP2 assoctest.dat 26612 GT
SAMP3 assoctest.dat 26613 GT
SAMP4 assoctest.dat 26600 GT
SAMP5 assoctest.dat 26600 GT
SAMP6 assoctest.dat 26603 GT
SAMP7 assoctest.dat 26584 GT
SAMP8 assoctest.dat 26612 GT
SAMP9 assoctest.dat 26585 GT
SAMP10 assoctest.dat 26613 GT
SAMP11 assoctest.dat 26588 GT
(3170 records omitted)
fields)Command vtools show fields) lists all variant info fields (fields in the master variant table) and annotation fields (fields provided by annotation databases). Although these fields are from different sources, they can be used in the same manner to identify and filter variants (c.f. vtools select). If you only need to see a list of available fields, you can use option -v0 to suppress comments.
% vtools show fields
variant.chr (char) Chromosome name (VARCHAR)
variant.pos (int) Position (INT, 1-based)
variant.ref (char) Reference allele (VARCHAR, - for missing allele of
an insertion)
variant.alt (char) Alternative allele (VARCHAR, - for missing allele of
an deletion)
variant.cnt (int)
variant.hom (int)
variant.het (int)
variant.other (int)
variant.num (int)
variant.missing (int)
variant.wtGT (int)
variant.mutGT (int)
variant.af (float)
You can use option -v0 to suppress comments (which can be long):
% vtools show fields -v0
variant.chr
variant.pos
variant.ref
variant.alt
variant.cnt
variant.hom
variant.het
variant.other
variant.num
variant.missing
variant.wtGT
variant.mutGT
variant.af
annotations and annotation)Command vtools show annotations displays all available annotation databases with their descriptions. Because of the growing number of annotation databases, the output of this command can be very long. You can however
--limit to limit the number of annotation database displayed, or-v 0 to suppress descriptions of databases.% vtools show annotations | head -50
CancerGeneCensus-20111215 Cancer Genome Project
CancerGeneCensus-20120315 Cancer Genome Project
CancerGeneCensus Cancer Genome Project
CosmicCodingMuts-v61_260912 Cosmic coding mutation database. This data
contains mutations affecting 10 or less nucleotides in
REF. The mutation data was obtained from the Sanger
Institute Catalogue Of Somatic Mutations In Cancer web
site, http://www.sanger.ac.uk/cosmic. Bamford et al
(2004). The COSMIC (Catalogue of Somatic Mutations in
Cancer) database and website. Br J Cancer, 91,355-358.
CosmicCodingMuts Cosmic coding mutation database. This data contains
mutations affecting 10 or less nucleotides in REF.
The mutation data was obtained from the Sanger
Institute Catalogue Of Somatic Mutations In Cancer web
site, http://www.sanger.ac.uk/cosmic. Bamford et al
(2004). The COSMIC (Catalogue of Somatic Mutations in
Cancer) database and website. Br J Cancer, 91,355-358.
CosmicMutantExport-v61_260912 Cosmic mutant export. This data contains all
coding point mutations. The mutation data was
obtained from the Sanger Institute Catalogue Of
Somatic Mutations In Cancer web site,
http://www.sanger.ac.uk/cosmic. Bamford et al (2004).
The COSMIC (Catalogue of Somatic Mutations in Cancer)
database and website. Br J Cancer, 91,355-358.
CosmicMutantExport Cosmic mutant export. This data contains all coding
point mutations. The mutation data was obtained from
the Sanger Institute Catalogue Of Somatic Mutations In
Cancer web site, http://www.sanger.ac.uk/cosmic.
Bamford et al (2004). The COSMIC (Catalogue of Somatic
Mutations in Cancer) database and website. Br J
Cancer, 91,355-358.
CosmicNonCodingVariants-v61_260912 Cosmic non-coding mutation database. This
data contains mutations affecting 10 or less
nucleotides in REF. The mutation data was obtained
from the Sanger Institute Catalogue Of Somatic
Mutations In Cancer web site,
http://www.sanger.ac.uk/cosmic. Bamford et al (2004).
The COSMIC (Catalogue of Somatic Mutations in Cancer)
database and website. Br J Cancer, 91,355-358.
CosmicNonCodingVariants Cosmic non-coding mutation database. This data
contains mutations affecting 10 or less nucleotides in
REF. The mutation data was obtained from the Sanger
Institute Catalogue Of Somatic Mutations In Cancer web
site, http://www.sanger.ac.uk/cosmic. Bamford et al
(2004). The COSMIC (Catalogue of Somatic Mutations in
Cancer) database and website. Br J Cancer, 91,355-358.
ccdsGene-hg19_20110909 CCDS Genes
ccdsGene-hg19_20111206 CCDS Genes
ccdsGene CCDS Genes
ccdsGene_exon-hg19_20110909 CCDS exons
You can list a subset of annotation databases by specifying one or more patterns:
% vtools show annotations thousand ccds
ccdsGene-hg19_20110909 CCDS Genes
ccdsGene-hg19_20111206 CCDS Genes
ccdsGene-hg19_20130904 High-confidence human gene annotations from the Consensus Coding
Sequence (CCDS) project.
ccdsGene-hg38_20171008 High-confidence human gene annotations from the Consensus Coding
Sequence (CCDS) project.
ccdsGene_exon-hg19_20110909 CCDS exons
ccdsGene_exon-hg19_20111206 CCDS exons
ccdsGene_exon-hg19_20130904 High-confidence human gene annotations from the Consensus Coding
Sequence (CCDS) project. This database contains all exon regions of the
CCDS genes.
ccdsGene_exon-hg38_20171008 CCDS exons
ccdsGene_exon_hg19-20111206 CCDS exons
ccdsGene_hg19-20111206 CCDS Genes
thousandGenomes-hg19_20130502 Phase 3 data of the thousand genomes project, created from
ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/release/20130502/ALL.wgs.p
hase3_shapeit2_mvncall_integrated_v5a.20130502.sites.vcf.gz
thousandGenomes-hg19_v3_20101123 1000 Genomes VCF file analyzed in March 2012 from data
generated from phase 1 of the project (available from: ftp://ftp.1000ge
nomes.ebi.ac.uk/vol1/ftp/release/20110521/ALL.wgs.phase1_release_v3.201
01123.snps_indels_sv.sites.vcf.gz).
thousandGenomes-hg19_v5b_20130502 1000 Genomes VCF file analyzed in February 2015 from data
generated from phase 1 of the project (available from: ftp://ftp.1000ge
nomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.wgs.phase3_shapeit2_mvnca
ll_integrated_v5b.20130502.sites.vcf.gz.)
If you only need to see a list annotation databases without description, you can pass the -v0 option,
% vtools show annotations gene -v0
CancerGeneCensus-20111215
CancerGeneCensus-20120315
CancerGeneCensus-20130711
CancerGeneCensus-20170912
EntrezGene-20131028
EntrezGene-20170919
EntrezGene2RefSeq-20131028
EntrezGene2RefSeq-20170919
ccdsGene-hg19_20110909
ccdsGene-hg19_20111206
ccdsGene-hg19_20130904
ccdsGene-hg38_20171008
ccdsGene_exon-hg19_20110909
ccdsGene_exon-hg19_20111206
ccdsGene_exon-hg19_20130904
ccdsGene_exon-hg38_20171008
ccdsGene_exon_hg19-20111206
ccdsGene_hg19-20111206
dbNSFP_gene-2_0
dbNSFP_gene-2_1
dbNSFP_gene-2_3
dbNSFP_gene-2_4
dbNSFP_gene-2_7
dbNSFP_gene-3_5a
knownGene-hg18_20110909
knownGene-hg18_20121219
knownGene-hg19_20110909
knownGene-hg19_20121219
knownGene-hg19_20130904
knownGene-hg38_20160328
knownGene_exon-hg18_20110909
knownGene_exon-hg19_20110909
knownGene_exon-hg19_20130904
knownGene_exon-hg38_20160328
refGene-hg18_20110909
refGene-hg19_20110909
refGene-hg19_20130904
refGene-hg38_20170201
refGene-mm10_20141201
refGene_coding-hg19_20130904
refGene_exon-hg18_20110909
refGene_exon-hg19_20110909
refGene_exon-hg19_20130904
refGene_exon-mm10_20141201
refGene_exon-mm10_20171008
After using an annotation database with command vtools use, you can view the details of the annotation database using command vtools show annotation ANNODB. By default, this command displays basic information of the annotation database (type, number of records etc), and name and comment of each annotation field. If an -v 2 option is specified, it will also list the details of each fields, including range, unique values, and number of missing values.
% vtools show annotation knownGene
Annotation database knownGene (version hg19_20121219)
Description: UCSC Known Genes
Database type: range
Reference genome hg19: chr, txStart, txEnd
name Name of gene such as uc001aaa.3
chr
strand which DNA strand contains the observed alleles
txStart Transcription start position
txEnd Transcription end position
cdsStart Coding region start
cdsEnd Coding region end
exonCount Number of exons
% vtools show annotation knownGene -v2
DEBUG:
DEBUG: show annotation knownGene -v2
DEBUG: Using temporary directory /tmp/tmp3fjnagg2/_tmp_135971
Annotation database knownGene (version hg19_20130904)
Description: Gene predictions based on data from RefSeq, Genbank, CCDS and UniProt, from the
UCSC KnownGene track.
Database type: range
Number of records: 82,960
Distinct ranges: 60,726
Reference genome hg19: chr, txStart, txEnd
Field: name
Type: string
Comment: Name of gene such as uc001aaa.3
Missing entries: 0
Unique Entries: 82,960
Field: chr
Type: string
Missing entries: 0
Unique Entries: 60
Field: strand
Type: string
Comment: which DNA strand contains the observed alleles
Missing entries: 0
Unique Entries: 2
Field: txStart
Type: integer
Comment: Transcription start position
Missing entries: 0
Unique Entries: 48,720
Range: 1 - 249211537
Field: txEnd
Type: integer
Comment: Transcription end position
Missing entries: 0
Unique Entries: 48,713
Range: 368 - 249213345
Field: cdsStart
Type: integer
Comment: Coding region start
Missing entries: 0
Unique Entries: 51,789
Range: 1 - 249211537
Field: cdsEnd
Type: integer
Comment: Coding region end
Missing entries: 0
Unique Entries: 51,745
Range: 0 - 249212562
Field: exonCount
Type: integer
Comment: Number of exons
Missing entries: 0
Unique Entries: 119
Range: 1 - 5065
track)variant tools supports the use of annotation tracks to annotate and select variants. These tracks can be in tabix-indexed vcf files, indexed BAM file, bigBed and bigWig format and provides differnt fields through the second parameter of function track(filename, field). Command vtools show track is provided to display the details of each track file.
% vtools show track CEU_hg38.vcf | head -30
Version VCF v4.0
Number of fields: 69
Header: (exclude INFO and FORMAT lines)
##reference=human_b36_both.fasta
##rsIDs=dbSNP b129 mapped to NCBI 36.3, August 10, 2009
Available columns (with default type VARCHAR):
0 (INTEGER) 1 if matched
chr (1, chrom) chromosome
pos (2 for INTEGER) position (1-based)
name (3) name of variant
ref (4) reference allele
alt (5) alternative alleles
qual (6) qual
filter (7) filter
info (8, default) variant info fields
info.DP Total Depth
info.HM2 HapMap2 membership
info.HM3 HapMap3 membership
info.AA Ancestral Allele, ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/pilot_data/technical/reference/ancestral_alignments/README
info.AC Allele count in genotypes
info.AN Total number of alleles in called genotypes
format (9) genotype format
NA06985 (10) genotype for sample NA06985
NA06985.GT Genotype for sample NA06985
NA06985.DP Read Depth for sample NA06985
NA06985.CB Called by S(Sanger), M(UMich), B(BI) for sample NA06985
NA06986 (11) genotype for sample NA06986
NA06986.GT Genotype for sample NA06986
Although cannot be used as track files, vtools show track can display information of plain vcf file (not compressed, with extension .vcf), which can be used to show useful information of the header of such files.
% vtools show track http://ftp-trace.ncbi.nih.gov/1000genomes/ftp/release/20110521/ALL.chr1.phase1_release_v3.20101123.snps_indels_svs.genotypes.vcf.gz | head -30
Version VCF v4.1
Number of fields: 1101
Header: (exclude INFO and FORMAT lines)
##ALT=<ID=DEL,Description="Deletion">
##reference=GRCh37
##reference=GRCh37
Available columns (with default type VARCHAR):
0 (INTEGER) 1 if matched
chr (1, chrom) chromosome
pos (2 for INTEGER) position (1-based)
name (3) name of variant
ref (4) reference allele
alt (5) alternative alleles
qual (6) qual
filter (7) filter
info (8, default) variant info fields
info.LDAF MLE Allele Frequency Accounting for LD
info.AVGPOST Average posterior probability from MaCH/Thunder
info.RSQ Genotype imputation quality from MaCH/Thunder
info.ERATE Per-marker Mutation rate from MaCH/Thunder
info.THETA Per-marker Transition rate from MaCH/Thunder
info.CIEND Confidence interval around END for imprecise variants
info.CIPOS Confidence interval around POS for imprecise variants
info.END End position of the variant described in this record
info.HOMLEN Length of base pair identical micro-homology at event breakpoints
info.HOMSEQ Sequence of base pair identical micro-homology at event breakpoints
info.SVLEN Difference in length between REF and ALT alleles
info.SVTYPE Type of structural variant
% vtools show track wgEncodeDukeDnase8988T.fdr01peaks.hg19.bb
Version: 4
Item count: 196180
Primary data size: 1806867
Zoom levels: 8
Chrom count: 23
Chrom size:
chr1 249250621
chr10 135534747
chr11 135006516
chr12 133851895
chr13 115169878
chr14 107349540
chr15 102531392
chr16 90354753
chr17 81195210
chr18 78077248
chr19 59128983
chr2 243199373
chr20 63025520
chr21 48129895
chr22 51304566
chr3 198022430
chr4 191154276
chr5 180915260
chr6 171115067
chr7 159138663
chr8 146364022
chr9 141213431
chrX 155270560
Bases covered 29405430
Mean depth: 1.000734
Min depth: 1.000000
Max depth: 2.000000
Std of depth: 0.027074
Number of fields: 10
Available columns (with default type VARCHAR):
chrom (1) Name of the chromosome (or contig, scaffold, etc.).
chromStart (2 as INTEGER) The starting position of the feature in the chromosome
or scaffold. The first base in a chromosome is numbered
0.
chromEnd (3 as INTEGER) The ending position of the feature in the chromosome or
scaffold. The chromEnd base is not included in the display
of the feature. For example, the first 100 bases of a chromosome
are defined as chromStart=0, chromEnd=100, and span the
bases numbered 0-99.
name (4) Name given to a region (preferably unique). Use '.' if no
name is assigned.
score (5 as INTEGER) Indicates how dark the peak will be displayed in the browser
(0-1000). If all scores were '0' when the data were submitted
to the DCC, the DCC assigned scores 1-1000 based on signal
value. Ideally the average signalValue per base spread
is between 100-1000.
strand (6) +/- to denote strand or orientation (whenever applicable).
Use '.' if no orientation is assigned.
signalValue (7 as FLOAT) Measurement of overall (usually, average) enrichment for
the region
pValue (8 as FLOAT) Measurement of statistical significance (-log10, -1 if no
pValue is assigned)
qValue (9 as FLOAT) Measurement of statistical significance using false discovery
rate (-log10, -1 if no qValue is assigned)
peak (10 as INTEGER) Point-source called for this peak; 0-based offset from chromStart
(-1 if no point-source called)
% vtools show track ~/vtools/wgEncodeGisRnaSeqH1hescCellPapPlusRawRep1.bigWig
Version: 4
Primary data size 226114375
Zoom levels: 10
Chrom count: 25
Chrom size:
chr1 249250621
chr10 135534747
chr11 135006516
chr12 133851895
chr13 115169878
chr14 107349540
chr15 102531392
chr16 90354753
chr17 81195210
chr18 78077248
chr19 59128983
chr2 243199373
chr20 63025520
chr21 48129895
chr22 51304566
chr3 198022430
chr4 191154276
chr5 180915260
chr6 171115067
chr7 159138663
chr8 146364022
chr9 141213431
chrM 16571
chrX 155270560
chrY 59373566
Bases covered: 84281746
Mean: 10.253978
Min: 1.000000
Max: 46751.000000
std: 119.977095
Number of fields: 4
Available columns (with default type VARCHAR):
0 (INTEGER) 1 if matched
chrom (1) chromosome
chromStart (2 as INTEGER) start position (0-based)
chromEnd (3 as INTEGER) end position (1-based)
value (4 as FLOAT) value
% vtools show track ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data/HG00096/alignment/HG00096.chrom11.ILLUMINA.bwa.GBR.low_coverage.20120522.bam
[bam_index_load] attempting to download the remote index file.
[bam_index_load] attempting to download the remote index file.
Header:
@HD VN:1.0 SO:coordinate
@SQ SN:1 LN:249250621 M5:1b22b98cdeb4a9304cb5d48026a85128 UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:2 LN:243199373 M5:a0d9851da00400dec1098a9255ac712e UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:3 LN:198022430 M5:fdfd811849cc2fadebc929bb925902e5 UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:4 LN:191154276 M5:23dccd106897542ad87d2765d28a19a1 UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:5 LN:180915260 M5:0740173db9ffd264d728f32784845cd7 UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:6 LN:171115067 M5:1d3a93a248d92a729ee764823acbbc6b UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:7 LN:159138663 M5:618366e953d6aaad97dbe4777c29375e UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:8 LN:146364022 M5:96f514a9929e410c6651697bded59aec UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:9 LN:141213431 M5:3e273117f15e0a400f01055d9f393768 UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:10 LN:135534747 M5:988c28e000e84c26d552359af1ea2e1d UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:11 LN:135006516 M5:98c59049a2df285c76ffb1c6db8f8b96 UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:12 LN:133851895 M5:51851ac0e1a115847ad36449b0015864 UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:13 LN:115169878 M5:283f8d7892baa81b510a015719ca7b0b UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:14 LN:107349540 M5:98f3cae32b2a2e9524bc19813927542e UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:15 LN:102531392 M5:e5645a794a8238215b2cd77acb95a078 UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:16 LN:90354753 M5:fc9b1a7b42b97a864f56b348b06095e6 UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:17 LN:81195210 M5:351f64d4f4f9ddd45b35336ad97aa6de UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:18 LN:78077248 M5:b15d4b2d29dde9d3e4f93d1d0f2cbc9c UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:19 LN:59128983 M5:1aacd71f30db8e561810913e0b72636d UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:20 LN:63025520 M5:0dec9660ec1efaaf33281c0d5ea2560f UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:21 LN:48129895 M5:2979a6085bfe28e3ad6f552f361ed74d UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:22 LN:51304566 M5:a718acaa6135fdca8357d5bfe94211dd UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:X LN:155270560 M5:7e0e2e580297b7764e31dbc80c2540dd UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:Y LN:59373566 M5:1fa3474750af0948bdf97d5a0ee52e51 UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:MT LN:16569 M5:c68f52674c9fb33aef52dcf399755519 UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:GL000207.1 LN:4262 M5:f3814841f1939d3ca19072d9e89f3fd7 UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:GL000226.1 LN:15008 M5:1c1b2cd1fccbc0a99b6a447fa24d1504 UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:GL000229.1 LN:19913 M5:d0f40ec87de311d8e715b52e4c7062e1 UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:GL000231.1 LN:27386 M5:ba8882ce3a1efa2080e5d29b956568a4 UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:GL000210.1 LN:27682 M5:851106a74238044126131ce2a8e5847c UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:GL000239.1 LN:33824 M5:99795f15702caec4fa1c4e15f8a29c07 UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:GL000235.1 LN:34474 M5:118a25ca210cfbcdfb6c2ebb249f9680 UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:GL000201.1 LN:36148 M5:dfb7e7ec60ffdcb85cb359ea28454ee9 UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:GL000247.1 LN:36422 M5:7de00226bb7df1c57276ca6baabafd15 UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:GL000245.1 LN:36651 M5:89bc61960f37d94abf0df2d481ada0ec UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:GL000197.1 LN:37175 M5:6f5efdd36643a9b8c8ccad6f2f1edc7b UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:GL000203.1 LN:37498 M5:96358c325fe0e70bee73436e8bb14dbd UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:GL000246.1 LN:38154 M5:e4afcd31912af9d9c2546acf1cb23af2 UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:GL000249.1 LN:38502 M5:1d78abec37c15fe29a275eb08d5af236 UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:GL000196.1 LN:38914 M5:d92206d1bb4c3b4019c43c0875c06dc0 UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:GL000248.1 LN:39786 M5:5a8e43bec9be36c7b49c84d585107776 UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:GL000244.1 LN:39929 M5:0996b4475f353ca98bacb756ac479140 UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:GL000238.1 LN:39939 M5:131b1efc3270cc838686b54e7c34b17b UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:GL000202.1 LN:40103 M5:06cbf126247d89664a4faebad130fe9c UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:GL000234.1 LN:40531 M5:93f998536b61a56fd0ff47322a911d4b UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:GL000232.1 LN:40652 M5:3e06b6741061ad93a8587531307057d8 UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:GL000206.1 LN:41001 M5:43f69e423533e948bfae5ce1d45bd3f1 UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:GL000240.1 LN:41933 M5:445a86173da9f237d7bcf41c6cb8cc62 UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:GL000236.1 LN:41934 M5:fdcd739913efa1fdc64b6c0cd7016779 UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:GL000241.1 LN:42152 M5:ef4258cdc5a45c206cea8fc3e1d858cf UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:GL000243.1 LN:43341 M5:cc34279a7e353136741c9fce79bc4396 UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:GL000242.1 LN:43523 M5:2f8694fc47576bc81b5fe9e7de0ba49e UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:GL000230.1 LN:43691 M5:b4eb71ee878d3706246b7c1dbef69299 UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:GL000237.1 LN:45867 M5:e0c82e7751df73f4f6d0ed30cdc853c0 UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:GL000233.1 LN:45941 M5:7fed60298a8d62ff808b74b6ce820001 UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:GL000204.1 LN:81310 M5:efc49c871536fa8d79cb0a06fa739722 UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:GL000198.1 LN:90085 M5:868e7784040da90d900d2d1b667a1383 UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:GL000208.1 LN:92689 M5:aa81be49bf3fe63a79bdc6a6f279abf6 UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:GL000191.1 LN:106433 M5:d75b436f50a8214ee9c2a51d30b2c2cc UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:GL000227.1 LN:128374 M5:a4aead23f8053f2655e468bcc6ecdceb UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:GL000228.1 LN:129120 M5:c5a17c97e2c1a0b6a9cc5a6b064b714f UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:GL000214.1 LN:137718 M5:46c2032c37f2ed899eb41c0473319a69 UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:GL000221.1 LN:155397 M5:3238fb74ea87ae857f9c7508d315babb UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:GL000209.1 LN:159169 M5:f40598e2a5a6b26e84a3775e0d1e2c81 UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:GL000218.1 LN:161147 M5:1d708b54644c26c7e01c2dad5426d38c UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:GL000220.1 LN:161802 M5:fc35de963c57bf7648429e6454f1c9db UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:GL000213.1 LN:164239 M5:9d424fdcc98866650b58f004080a992a UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:GL000211.1 LN:166566 M5:7daaa45c66b288847b9b32b964e623d3 UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:GL000199.1 LN:169874 M5:569af3b73522fab4b40995ae4944e78e UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:GL000217.1 LN:172149 M5:6d243e18dea1945fb7f2517615b8f52e UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:GL000216.1 LN:172294 M5:642a232d91c486ac339263820aef7fe0 UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:GL000215.1 LN:172545 M5:5eb3b418480ae67a997957c909375a73 UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:GL000205.1 LN:174588 M5:d22441398d99caf673e9afb9a1908ec5 UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:GL000219.1 LN:179198 M5:f977edd13bac459cb2ed4a5457dba1b3 UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:GL000224.1 LN:179693 M5:d5b2fc04f6b41b212a4198a07f450e20 UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:GL000223.1 LN:180455 M5:399dfa03bf32022ab52a846f7ca35b30 UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:GL000195.1 LN:182896 M5:5d9ec007868d517e73543b005ba48535 UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:GL000212.1 LN:186858 M5:563531689f3dbd691331fd6c5730a88b UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:GL000222.1 LN:186861 M5:6fe9abac455169f50470f5a6b01d0f59 UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:GL000200.1 LN:187035 M5:75e4c8d17cd4addf3917d1703cacaf25 UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:GL000193.1 LN:189789 M5:dbb6e8ece0b5de29da56601613007c2a UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:GL000194.1 LN:191469 M5:6ac8f815bf8e845bb3031b73f812c012 UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:GL000225.1 LN:211173 M5:63945c3e6962f28ffd469719a747e73c UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:GL000192.1 LN:547496 M5:325ba9e808f669dfeee210fdd7b470ac UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:NC_007605 LN:171823 M5:6743bd63b3ff2b5b8985d8933c53290a UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@SQ SN:hs37d5 LN:35477943 M5:5b6a4b3a81a2d3c134b7d14bf6ad39f1 UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human
@RG ID:SRR062634 LB:2845856850 SM:HG00096 PI:206 CN:WUGSC PL:ILLUMINA DS:SRP001294
@RG ID:SRR062635 LB:2845856850 SM:HG00096 PI:206 CN:WUGSC PL:ILLUMINA DS:SRP001294
@RG ID:SRR062641 LB:2845856850 SM:HG00096 PI:206 CN:WUGSC PL:ILLUMINA DS:SRP001294
@PG ID:bwa_index PN:bwa VN:0.5.9-r16 CL:bwa index -a bwtsw \\(reference_fasta
@PG ID:bwa_aln_fastq PN:bwa PP:bwa_index VN:0.5.9-r16 CL:bwa aln -q 15 -f \\(sai_file \\(reference_fasta \\(fastq_file
@PG ID:bwa_sam PN:bwa PP:bwa_aln_fastq VN:0.5.9-r16 CL:bwa sampe -a 618 -r \\(rg_line -f \\(sam_file \\(reference_fasta \\(sai_file(s) \\(fastq_file(s)
@PG ID:sam_to_fixed_bam PN:samtools PP:bwa_sam VN:0.1.17 (r973:277) CL:samtools view -bSu \\(sam_file | samtools sort -n -o - samtools_nsort_tmp | samtools fixmate /dev/stdin /dev/stdout | samtools sort -o - samtools_csort_tmp | samtools fillmd -u - \\(reference_fasta > \\(fixed_bam_file
@PG ID:gatk_target_interval_creator PN:GenomeAnalysisTK PP:sam_to_fixed_bam VN:1.2-29-g0acaf2d CL:java \\(jvm_args -jar GenomeAnalysisTK.jar -T RealignerTargetCreator -R \\(reference_fasta -o \\(intervals_file -known \\(known_indels_file(s)
@PG ID:bam_realignment_around_known_indels PN:GenomeAnalysisTK PP:gatk_target_interval_creator VN:1.2-29-g0acaf2d CL:java \\(jvm_args -jar GenomeAnalysisTK.jar -T IndelRealigner -R \\(reference_fasta -I \\(bam_file -o \\(realigned_bam_file -targetIntervals \\(intervals_file -known \\(known_indels_file(s) -LOD 0.4 -model KNOWNS_ONLY -compress 0 --disable_bam_indexing
@PG ID:bam_count_covariates PN:GenomeAnalysisTK PP:bam_realignment_around_known_indels VN:1.2-29-g0acaf2d CL:java \\(jvm_args -jar GenomeAnalysisTK.jar -T CountCovariates -R \\(reference_fasta -I \\(bam_file -recalFile \\(bam_file.recal_data.csv -knownSites \\(known_sites_file(s) -l INFO -L '1;2;3;4;5;6;7;8;9;10;11;12;13;14;15;16;17;18;19;20;21;22;X;Y;MT' -cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -cov DinucCovariate
@PG ID:bam_recalibrate_quality_scores PN:GenomeAnalysisTK PP:bam_count_covariates VN:1.2-29-g0acaf2d CL:java \\(jvm_args -jar GenomeAnalysisTK.jar -T TableRecalibration -R \\(reference_fasta -recalFile \\(bam_file.recal_data.csv -I \\(bam_file -o \\(recalibrated_bam_file -l INFO -compress 0 --disable_bam_indexing
@PG ID:bam_calculate_bq PN:samtools PP:bam_recalibrate_quality_scores VN:0.1.17 (r973:277) CL:samtools calmd -Erb \\(bam_file \\(reference_fasta > \\(bq_bam_file
@PG ID:bam_merge PN:picard PP:bam_calculate_bq VN:1.53 CL:java \\(jvm_args -jar MergeSamFiles.jar INPUT=$bam_file(s) OUTPUT=$merged_bam VALIDATION_STRINGENCY=SILENT
@PG ID:bam_mark_duplicates PN:picard PP:bam_merge VN:1.53 CL:java \\(jvm_args -jar MarkDuplicates.jar INPUT=$bam_file OUTPUT=$markdup_bam_file ASSUME_SORTED=TRUE METRICS_FILE=/dev/null VALIDATION_STRINGENCY=SILENT
@PG ID:bam_merge.1 PN:picard PP:bam_mark_duplicates VN:1.53 CL:java \\(jvm_args -jar MergeSamFiles.jar INPUT=$bam_file(s) OUTPUT=$merged_bam VALIDATION_STRINGENCY=SILENT
@CO $known_indels_file(s) = ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_mapping_resources/ALL.wgs.indels_mills_devine_hg19_leftAligned_collapsed_double_hit.indels.sites.vcf.gz
@CO $known_indels_file(s) .= ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_mapping_resources/ALL.wgs.low_coverage_vqsr.20101123.indels.sites.vcf.gz
@CO $known_sites_file(s) = ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_mapping_resources/ALL.wgs.dbsnp.build135.snps.sites.vcf.gz
Chrom size: 86
1 249250621
2 243199373
3 198022430
4 191154276
5 180915260
6 171115067
7 159138663
8 146364022
9 141213431
10 135534747
11 135006516
12 133851895
13 115169878
14 107349540
15 102531392
16 90354753
17 81195210
18 78077248
19 59128983
20 63025520
21 48129895
22 51304566
X 155270560
Y 59373566
MT 16569
GL000207.1 4262
GL000226.1 15008
GL000229.1 19913
GL000231.1 27386
GL000210.1 27682
GL000239.1 33824
GL000235.1 34474
GL000201.1 36148
GL000247.1 36422
GL000245.1 36651
GL000197.1 37175
GL000203.1 37498
GL000246.1 38154
GL000249.1 38502
GL000196.1 38914
GL000248.1 39786
GL000244.1 39929
GL000238.1 39939
GL000202.1 40103
GL000234.1 40531
GL000232.1 40652
GL000206.1 41001
GL000240.1 41933
GL000236.1 41934
GL000241.1 42152
GL000243.1 43341
GL000242.1 43523
GL000230.1 43691
GL000237.1 45867
GL000233.1 45941
GL000204.1 81310
GL000198.1 90085
GL000208.1 92689
GL000191.1 106433
GL000227.1 128374
GL000228.1 129120
GL000214.1 137718
GL000221.1 155397
GL000209.1 159169
GL000218.1 161147
GL000220.1 161802
GL000213.1 164239
GL000211.1 166566
GL000199.1 169874
GL000217.1 172149
GL000216.1 172294
GL000215.1 172545
GL000205.1 174588
GL000219.1 179198
GL000224.1 179693
GL000223.1 180455
GL000195.1 182896
GL000212.1 186858
GL000222.1 186861
GL000200.1 187035
GL000193.1 189789
GL000194.1 191469
GL000225.1 211173
GL000192.1 547496
NC_007605 171823
hs37d5 35477943
Tags that can be outputed or used in filters, with values from the 1st record:
X0 c (int8) : 10
X1 c (int8) : 0
MD Z (string) : 0A99
RG Z (string) : SRR062634
AM c (int8) : 0
NM c (int8) : 1
SM c (int8) : 0
MQ c (int8) : 0
XT A (char) : R
BQ Z (string) : C[Y@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
Parameters min_qual, min_mapq and TAG=VAL can be used to limit the reads to the
ones with mapq and qual scores that exceed the specified value, and with specified TAG.
The header of BAM track provides many important information about the bam file. You should consult the SAM format specification for the meaning of them, but briefly:
HD - header: VN is for file format version, SO for sort order, which can be unsorted, queryname or coordinate.SQ - Sequence dictionary: SN is sequence name, @LNis sequence length. This might repeat the chromome length information listed below.ASreference genome used for assembly,SP@@ for species.RG - Read group: ID for read group identifier, SM for sample, LB for library, DS for description, PU for platform unit, DT for date the run was produced, PL for platform (e.g. illumina).PG - Program: ID for program name, VN for program version, CL for command line.CO - CommentThe tags are also important if you need to filter reads by tag values. For example, RG can be used to differentiate reads that belong to different samples if the bam file contains reads from multiple samples.
formats and format)variant tools repository has a number of file format description files .fmt that defines a formats of files that can be used for commands vtools import, vtools update --from_file, and vtools export. To get a complete list of supported file formats, you can use command vtools show formats. Options -v0 and --limit are supported to suppress comment and limit number of formats to display, respectively.
% vtools show formats | head -50
CASAVA18_snps Input format illumina snps.txt file, created by CASAVA
version 1.8
(http://www.illumina.com/support/documentation.ilmn).
This format imports chr, pos, ref, alt of most likely
genotype, and a Q score for the most likely genotype.
plink Input format for PLINK dataset. Currently only PLINK
binary PED file format is supported (*.bed, *.bim &
*.fam)
ANNOVAR Input format of ANNOVAR. No genotype is defined.
pileup_indel Input format for samtools pileup indel caller. This
format imports chr, pos, ref, alt and genotype.
ANNOVAR_exonic_variant_function Output from ANNOVAR, generated from command
"path/to/annovar/annotate_variation.pl annovar.txt
path/to/annovar/humandb/". This format imports chr,
pos, ref, alt and ANNOVAR annotations. For details
please refer to http://www.openbioinformatics.org/anno
var/annovar_gene.html
ANNOVAR_variant_function Output from ANNOVAR for files of type
"*.variant_function", generated from command
"path/to/annovar/annotate_variation.pl annovar.txt
path/to/annovar/humandb/". This format imports chr,
pos, ref, alt and ANNOVAR annotations. For details
please refer to http://www.openbioinformatics.org/anno
var/annovar_gene.html
CGA Input format from Complete Genomics Variant file
masterVarBeta-[ASM-ID].tsv.bz2, created by Complete
Genomcis Analysis Tools (GSA Tools 1.5 or eariler,
http://www.completegenomics.com/sequence-
data/cgatools/, http://media.completegenomics.com/docu
ments/DataFileFormats+Standard+Pipeline+2.0.pdf). This
format imports chr, pos, ref, alt of only variants
that have been fully called and are not equals to ref.
(E.g. records with zygosity equal to no-call and half,
and varType equal to ref are discarded.)
map This input format imports variants from files in MAP
format (with columns chr, name gen_dist, pos), or any
delimiter-separated format with columns chr and pos.
Because these input files do not contain reference and
alternative alleles of variants, this format queries
such information from the dbSNP database using chr and
pos. Records that does not exist in dbSNP will be
discarded. Records with multiple alternative alleles
will lead to multiple records.
polyphen2 To be used to export variants in a format that is
acceptable by the polyphen2 server
http://genetics.bwh.harvard.edu/pph2/bgi.shtml, and to
import the FULL report returned by this server.
basic A basic variant input format with four columns: chr,
pos, ref, alt.
vcf Import vcf
Comments can be suppressed using option -v0,
% vtools show formats -v0
CASAVA18_snps
plink
ANNOVAR
pileup_indel
ANNOVAR_exonic_variant_function
ANNOVAR_variant_function
CGA
map
polyphen2
basic
vcf
CASAVA18_indels
csv
tped
You can use command vtools show format FMT to list the details of a format. Note that
Columns are used to direct output. If no column is specified, the format cannot be used for command vtools export.variant, position, and range. Command vtools import can only import data from variant-based files (because it imports variants). In comparison, command vtools update can update existing variant using all three types of input files.% vtools show format map
Format: map
Description: This input format imports variants from files in MAP
format (with columns chr, name gen_dist, pos), or any delimiter-separated
format with columns chr and pos. Because these input files do not contain
reference and alternative alleles of variants, this format queries such
information from the dbSNP database using chr and pos. Records that does not
exist in dbSNP will be discarded. Records with multiple alternative alleles
will lead to multiple records.
Columns:
None defined, cannot export to this format
variant:
chr Chromosome
pos 1-based position
ref Reference allele, '-' for insertion.
alt Alternative allele obtained from another database
Format parameters:
db_file (default: dbSNP.DB)
pos_idx Index of column for pyhysical location in the map
file, should be 4 for a standard map file with chr,
pos, gen_dist, pos. (default: 4)
ref_field Name of ref field from the annotation database, used
to retrieve reference allele at specified location.
(default: refNCBI)
alt_field Name of alt field from the annotation database, used
to retrieve alternative allele at specified location.
(default: alt)
chr_field Name of chr field from the annotation database, used
to locate variants from the dbSNP database. (default:
chr)
pos_field Name of pos field from the annotation database, used
to locate variants from the dbSNP database. (default:
start)
separator Separator of the input file, default to space or tab.
(default: None)
tests and test)Command vtools show tests shows a list of association tests that can be used in command vtools associate. Similar to other commands, option -v0 and --limit can be used to suppress description of tests and limit the number of tests to display.
% vtools show tests
BurdenBt Burden test for disease traits, Morris & Zeggini 2009
BurdenQt Burden test for quantitative traits, Morris & Zeggini
2009
CFisher Fisher's exact test on collapsed variant loci, Li &
Leal 2008
Calpha c-alpha test for unusual distribution of variants
between cases and controls, Neale et al 2011
CollapseBt Collapsing method for disease traits, Li & Leal 2008
CollapseQt Collapsing method for quantitative traits, Li & Leal
2008
GroupStat Calculates basic statistics for each testing group
GroupWrite Write data to disk for each testing group
KBAC Kernel Based Adaptive Clustering method, Liu & Leal
2010
LinRegBurden A versatile framework of association tests for
quantitative traits
LogitRegBurden A versatile framework of association tests for disease
traits
RBT Replication Based Test for protective and deleterious
variants, Ionita-Laza et al 2011
RTest A general framework for association analysis using R
programs
RareCover A "covering" method for detecting rare variants
association, Bhatia et al 2010.
SKAT SKAT (Wu et al 2011) and SKAT-O (Lee et al 2012)
SSeq_common Score statistic / SCORE-Seq software (Tang & Lin
2011), for common variants analysis
SSeq_rare Score statistic / SCORE-Seq software (Tang & Lin
2011), for rare variants analysis
VTtest VT statistic for disease traits, Price et al 2010
VariableThresholdsBt Variable thresholds method for disease traits, in the
spirit of Price et al 2010
VariableThresholdsQt Variable thresholds method for quantitative traits, in
the spirit of Price et al 2010
WSSRankTest Weighted sum method using rank test statistic, Madsen
& Browning 2009
WeightedBurdenBt Weighted genotype burden tests for disease traits,
using one or many arbitrary external weights as well
as one of 4 internal weighting themes
WeightedBurdenQt Weighted genotype burden tests for quantitative
traits, using one or many arbitrary external weights
as well as one of 4 internal weighting themes
aSum Adaptive Sum score test for protective and deleterious
variants, Han & Pan 2010
Display only the first 5 tests without description:
% vtools show tests -v0 -l 5
BurdenBt
BurdenQt
CFisher
Calpha
CollapseBt
(19 records omitted)
If you are interested in more details of a particular test, you can use command vtools show test TEST. This should give you a detailed description of the test, and all the options the test accept.
% vtools show test LogitRegBurden
Name: LogitRegBurden
Description: A versatile framework of association tests for disease traits
usage: vtools associate --method LogitRegBurden [-h] [--name NAME]
[-q1 MAFUPPER] [-q2 MAFLOWER]
[--alternative TAILED]
[--use_indicator] [-p N]
[--permute_by XY]
[--adaptive C]
[--variable_thresholds]
[--extern_weight [EXTERN_WEIGHT [EXTERN_WEIGHT ...]]]
[--weight {Browning_all,Browning,KBAC,RBT}]
[--NA_adjust]
[--moi {additive,dominant,recessive}]
Logistic regression test. p-value is based on the significance level of the
regression coefficient for genotypes. If --group_by option is specified, it
will collapse the variants within a group into a generic genotype score
optional arguments:
-h, --help show this help message and exit
--name NAME Name of the test that will be appended to names of
output fields, usually used to differentiate output of
different tests, or the same test with different
parameters.
-q1 MAFUPPER, --mafupper MAFUPPER
Minor allele frequency upper limit. All variants
having sample MAF<=m1 will be included in analysis.
Default set to 1.0
-q2 MAFLOWER, --maflower MAFLOWER
Minor allele frequency lower limit. All variants
having sample MAF>m2 will be included in analysis.
Default set to 0.0
--alternative TAILED Alternative hypothesis is one-sided ("1") or two-sided
("2"). Default set to 1
--use_indicator This option, if evoked, will apply binary coding to
genotype groups (coding will be "1" if ANY locus in
the group has the alternative allele, "0" otherwise)
-p N, --permutations N
Number of permutations
--permute_by XY Permute phenotypes ("Y") or genotypes ("X"). Default
is "Y"
--adaptive C Adaptive permutation using Edwin Wilson 95 percent
confidence interval for binomial distribution. The
program will compute a p-value every 1000 permutations
and compare the lower bound of the 95 percent CI of
p-value against "C", and quit permutations with the
p-value if it is larger than "C". It is recommended to
specify a "C" that is slightly larger than the
significance level for the study. To disable the
adaptive procedure, set C=1. Default is C=0.1
--variable_thresholds
This option, if evoked, will apply variable thresholds
method to the permutation routine in burden test on
aggregated variant loci
--extern_weight [EXTERN_WEIGHT [EXTERN_WEIGHT ...]]
External weights that will be directly applied to
genotype coding. Names of these weights should be in
one of '--var_info' or '--geno_info'. If multiple
weights are specified, they will be applied to
genotypes sequentially. Note that all weights will be
masked if --use_indicator is evoked.
--weight {Browning_all,Browning,KBAC,RBT}
Internal weighting themes inspired by various
association methods. Valid choices are:
'Browning_all', 'Browning', 'KBAC' and 'RBT'. Except
for 'Browning_all' weighting, tests using all other
weighting themes has to calculate p-value via
permutation. For details of the weighting themes,
please refer to the online documentation.
--NA_adjust This option, if evoked, will replace missing genotype
values with a score relative to sample allele
frequencies. The association test will be adjusted to
incorporate the information. This is an effective
approach to control for type I error due to
differential degrees of missing genotypes among
samples.
--moi {additive,dominant,recessive}
Mode of inheritance. Will code genotypes as 0/1/2/NA
for additive mode, 0/1/NA for dominant or recessive
mode. Default set to additive
snapshots and snapshot)You can save snapshots of the current project and revert to them later. This allows you to recover a project when it is damaged by wrong operations or system failure, and more importantly, allows you to explore different processing pipelines with a saved baseline stage. The command vtools show snapshots lists information about all snapshots. Names starting with vt_ are online snapshots that will be downloaded automatically using command vtools admin --load_snapshot NAME. These snapshots contain sample projects and data and are ideal for learning variant tools.
Note that:
vtools show snapshots.vtools admin --save_snapshot) can be saved in any directory and will not be listed by command vtools show snapshots. Command vtools show snapshot FILENAME can be used to show details of such snapshots.% vtools show snapshots
vt_qc snapshot for QC tutorial, exome data of 1000 genomes
project with simulated GD and GQ scores (online
snapshot)
vt_ExomeAssociation Data with ~26k variants from chr1 and 2, ~3k samples,
3 phenotypes, ready for association testing. (online
snapshot)
vt_quickStartGuide A simple project with variants from the CEU and JPT
pilot data of the 1000 genome project (online
snapshot)
vt_illuminaTestData Test data with 1M paired reads (online snapshot)
vt_simple A simple project with variants imported from three vcf
files (online snapshot)
vt_testData An empty project with some test datasets (online
snapshot)
If we create a snapshot,
% vtools admin --save_snapshot test1 'a test snapshot'
INFO: Copying genotypes
INFO: Snapshot test1 has been saved
It will be displayed in the list
% vtools show snapshots
test1 a test snapshot (created: Jul12 16:37:00)
vt_ExomeAssociation Data with ~26k variants from chr1 and 2, ~3k samples,
3 phenotypes, ready for association testing.
(created: Jul12 03:35:50)
vt_qc snapshot for QC tutorial, exome data of 1000 genomes
project with simulated GD and GQ scores (online
snapshot)
vt_ExomeAssociation Data with ~26k variants from chr1 and 2, ~3k samples,
3 phenotypes, ready for association testing. (online
snapshot)
vt_quickStartGuide A simple project with variants from the CEU and JPT
pilot data of the 1000 genome project (online
snapshot)
vt_illuminaTestData Test data with 1M paired reads (online snapshot)
vt_simple A simple project with variants imported from three vcf
files (online snapshot)
vt_testData An empty project with some test datasets (online
snapshot)
Such local snapshots are stored in the project cache directory and are listed automatically. However, if you create a local snapshot by specifying a filename (with suffix .tar or .tar.gz), such snapshots will not be displayed.
% vtools admin --save_snapshot local_snapshot.tar 'a local snapshot'
INFO: Copying genotypes
INFO: Snapshot local_snapshot.tar has been saved
% vtools show snapshots -l 2 -v0
test1
vt_ExomeAssociation
You can show the details of such snapshots using command vtools show snapshot NAME though.
% vtools show snapshot local_snapshot.tar
Name: local_snapshot.tar
Source: local
Creation date: Jul12 16:39:24
Description: a local snapshot
runtime_options and runtime_option)variant tools provides a number of runtime options that can be used to fine-tune the behavior of commands. You can use command vtools show runtime_options to get the name and description of these options. If you simply need to see a list of options, you can pass option -v0 to suppress descriptions. Please see command vtools admin --set_runtime_option for details.
% vtools show runtime_options | head -50
associate_num_of_readers None (default)
Use specified number of processes to read genotype
data for association tests. The default value is the
minimum of value of option --jobs and 8. Note that a
large number of reading processes might lead to
degraded performance or errors due to disk access
limits.
association_timeout None (default)
Cancel associate test and return special values when a
test lasts more than specified time (in seconds). The
default value of this option is None, which stands for
no time limit.
import_num_of_readers 2 (default)
variant tools by default uses two processes to read
from input files during multi-process importing
(--jobs > 0). You can want to set it to zero if a
single process provides better performance or reduces
disk traffic.
local_resource ~/.variant_tools (default)
A directory to store variant tools related resources
such as reference genomes and annotation database.
Files under this directory is usually downloaded
automatically upon use, but can also be synchronized
directly from
http://vtools.houstonbioinformatics.org/.
logfile_verbosity 2 (default)
Verbosity level of the log file, can be 0 for warning
and error only, 1 for general information, or 2 for
general and debug information.
search_path .;http://vtools.houstonbioinformatics.org/ (default)
A ;-separated list of directories and URLs that are
used to locate annotation database (.ann, .DB), file
format (.fmt) and other files. Reset this option
allows alternative local or online storage of such
files. variant tools will append trailing directories
such as annoDB for certain types of data so only root
directories should be listed in this search path.
sqlite_pragma (default)
pragmas for sqlite database that can be used to
optimize the performance of database operations.
temp_dir None (default)
Use the specified temporary directory to store
temporary files to improve performance (use separate
disks for project and temp files), or avoid problems
due to insufficient disk space.
treat_missing_as_wildtype False (default)
Treat missing values as wildtype alleles for
association tests. This option is used when samples
are called individuals or in batch so genotypes for
some samples are ignored and treated as missing if
to see a list of runtime options, use command
% vtools show runtime_options -v0
associate_num_of_readers
association_timeout
import_num_of_readers
local_resource
logfile_verbosity
search_path
sqlite_pragma
temp_dir
treat_missing_as_wildtype
verbosity
Furthermore, if you only need to check the exiting value of a runtime option, you can use command vtools show runtime_option OPT,
% vtools show runtime_option local_resource
~/.variant_tools