Installation
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Key concepts
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Vtools commands
init
Import
update
phenotype
lifttover
show
use
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exclude
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associate
output
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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
Formats
basic
csv
plink
rsname
cumtomized
tped
map
ANNNOVAR
CGA
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CASAVA18Indels
functor
ANNNOVAR variants
ANNNOVAR variants
Utilities
report progress
md5sumd
Application
Annotation
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Customized
Genes
ccdsGene
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Variants
COSMIC
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database
ESP
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EBI
Regions
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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
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Github repo
ScriptOfScripts
bpeng@mdanderson.org
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>
Application
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Association
> Basic statistics
Basic statistics
Basic statistics
Basic statistics
GroupStat&Write