Installation
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Key concepts
Supported types of variants
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
Introduction
Customized simulations
Models
Peng2014_ex1
Peng2014_ex2
Format
Formats
basic
csv
plink
rsname
Cumtomized
tped
map
Pipelines
Introduction
Customized pipeline
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
Utilities
report_progress
md5sumd
Application
Annotation
Introduction
Tutorial
Customized annotation databases
Genes
ccdsGene
Hugo gene
EntrezGene
knownGene
refGene
CancerGeneCensus
Variants
COSMIC
sbNSFP
dbSNP
linkage-physical map
Database of Genomic Variants
Exome Sequencing Project
gwasCatalog
HapMap
Thousand Genomes
Regions
Low complexity regions
Phast cons
Genomic super dups
cytoBand
Misc
Illumina
keggPathway
ENCODE
Discovery
Association
Introduction
Data exploration/QC
Association analysis
Post-assoc analysis
Basic data statistics
Group stat&Write
Single variant analysis
Fisher exact test
Single gene association methods
Introduction
CMC test
C-alpha test
KBAC test
RBT test
RareCover test
VT test
WSS test
aSum test
Joint/Conditional association analysis
Collapsing methods
Aggregation methods
Weighted methods
Variable thresholds
SKAT test
MetaSKAT analysis
VAT stacking
Create your test!
Running R programs
Programming in VAT
View association result
QQ plot and Manhattan plot
Development
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Github repo
ScriptOfScripts
bpeng@mdanderson.org
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