Installation
Documentation
Key concepts
Tutorials
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Vtools commands
init
Import
update
phenotype
lifttover
show
use
select
exclude
compare
associate
output
export
remove
execute
admin
Functions
ref_sequence
mut_sequence
track
genotype
samples
in_table
other functions
Vtools report
avg_depth
discordance_rate
sam_info
sequence
trans_ratio
variant_stat
inbreeding_coefficient
transmission
meta_analysis
plot_fields
plot_geno_fields
plot_pheno_fields
plot_association
Customization
Simulation
Customized
Models
Peng2014_ex1
Peng2014_ex2
Format
Pipelines
Customized
Variant calling
bwa_gatk33_hg19
bat_gatk33_b37
bwa_gatk28_hg19
bwa_gatk28_b37
Other pipelines
import_vcf
anno_utils
transmission
illumnina
ANNOVAR
snpEff
KING
filtering
Utilities
report progress
md5sumd
Application
Annotation
Tutorial
Customized
Genes
ccdsGene
HugoGene
EntrezGene
knownGene
refGene
CancerGeneCensus
Variants
COSMIC
dbNSFP
dbSNP
Rutgers map
database
ESP
gwasCatalog
hapmap
thousandGenomes
EBI
Regions
low complexity regions
PhastCons
genomicSuperDups
cytoBand
Misc
Illumina
keggPathway
ENCODE
Discovery
Association
QC
Association analysis
Post-assoc analysis
Basic statistics
GroupStat&Write
Single variant
Fisher exact test
Single gene
CMC test
C-alpha test
KBAC test
RBT test
RareCover test
VT test
WSS test
aSum test
Multivariate
collapsing
aggregation
weighted
variable thresholds
SKAT test
MetaSKAT
VAT stacking
Create your test!
running R programs
programming in VAT
View association result
Development
ChangeLog
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Under development
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Github repo
ScriptOfScripts
bpeng@mdanderson.org
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Regions
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Low Complexity and RepetitiveRegions
Low Complexity Regions
low complexity regions
Low Complexity and RepetitiveRegions
Low Complexity Regions