Vt

Introduction

vt is a tool set that calls, genotypes and filters short variants. It provides profiling of variants to aid in QC.

Location

Internal usage

 /net/fantasia/home/atks/programs/vtools/vt

External usage

 download from sourceforge/github

Discovery

Discovery is performed at per sample level, the evidence sites lists for each sample is then merged and site discovery statistics are computed. The user then makes a decision on cut offs to make to create an initial site list.

Generates site list with info fields E and N.

vt discover -i NA12878.bam -o NA12878.sites.vcf -g hs37d5.fa

Left align variants.

vt left_align -i NA12878.bam -o NA12878.leftaligned.sites.vcf -g hs37d5.fa

Evidence site lists are combined across samples and split by sites.

vt merge_and_split_sample_vcf -i NA12878.sites.vcf,NA12879.sites.vcf,NA12880.sites.vcf -o 1-1000000.sites.vcf

Discovery statistics are computed.

vt compute_discovery_stats -i 1-1000000.sites.vcf -o 1-1000000.annotated.sites.vcf 

A calling pipeline implemented in a make file is available here.

Genotyping

Each individual is genotyped at a set of sites.

vt genotype -i NA12878.bam -o NA12878.sites.vcf -g hs37d5.fa

Genotype sample VCFs are combined across samples and split by sites.

vt merge_and_split_sample_vcf -i NA12878.sites.vcf,NA12879.sites.vcf,NA12880.sites.vcf -o 1-1000000.sites.vcf

Features are computed.

vt compute_features -i 1-1000000.sites.vcf -o 1-1000000.annotated.sites.vcf 

A genotyping pipeline implemented in a make file is available here.

Filtering

Requires a set of features

vt  svm NA12878.bam -i NA12878.sites.vcf -o NA12878.svm.sites.vcf --pos positive.sites.vcf --neg negative.sites.vcf

A filtering pipeline implemented in a make file is available here.

Left Alignment

Left align indel type variants in a VCF file.

vt leftalign -i mills.vcf -o mills.leftaligned.vcf

Profile SNPs

Profile SNPs.

vt profile_snps -i mills.snps.sites.vcf

Profile Indels

Profile indels.

vt profile_indels -i mills.indels.sites.vcf

Profile MNPs

Profile MNPs.

vt profile_mnps -i mills.mnps.sites.vcf

sort

Sort variants according to contig lists in header.

vt sort -i mills.sites.vcf

split_by_variant

Split VCF files by variant type.

vt split_by_variant -i mills.sites.vcf

compute_<feature>

Compute feature of variant.

vt compute_feature -i mills.vcf

Resource Files

dbSNP OMNI 1000G Mills HAPMAP