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| === Introduction ===
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| vt is a tool set that calls, genotypes and filters short variants. It provides profiling of variants to aid in QC.
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| === Location ===
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| Internal usage
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| /net/fantasia/home/atks/programs/vtools/vt
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| External usage
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| download from sourceforge/github
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| === Discovery ===
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| Discovery is performed at per sample level, the evidence sites lists for each sample are then merged and site discovery statistics are computed.
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| The user then makes a decision on cut offs to make to create an initial candidate site list.
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| Generates site list with info fields E and N.
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| vt discover -i NA12878.bam -o NA12878.sites.vcf -g hs37d5.fa
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| Left align variants. This is required as left alignment if insertions and/or deletions within a read is sometimes insufficient to ensure complete left alignment.
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| vt left_align -i NA12878.bam -o NA12878.leftaligned.sites.vcf -g hs37d5.fa
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| Evidence site lists are combined across samples and split by sites to allow for parallelization.
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| vt merge_and_split_sample_vcf -i NA12878.sites.vcf,NA12879.sites.vcf,NA12880.sites.vcf -l 5000
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| Discovery statistics are computed. These statistics will allow you to choose a suitable cut off for creating a suitable candidate site list.
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| vt compute_discovery_stats -i 1-1000000.sites.vcf -o 1-1000000.annotated.sites.vcf
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| Merge site lists.
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| vt merge -i 1000000.sites.vcf,2000000.sites.vcf,3000000.sites.vcf -o candidate.sites.vcf
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| Plot charts to help with candidate list selection criteria.
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| vt plot_discovery -i candidate.sites.vcf
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| A calling pipeline implemented in a make file is available here.
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| === Genotyping ===
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| Each individual is genotyped at a set of sites.
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| vt genotype -i NA12878.bam -o NA12878.sites.vcf -g hs37d5.fa
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| Genotype sample VCFs are combined across samples and split by sites.
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| vt merge_and_split_sample_vcf -i NA12878.sites.vcf,NA12879.sites.vcf,NA12880.sites.vcf -o 1-1000000.sites.vcf
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| Features are computed.
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| vt compute_features -i 1-1000000.sites.vcf -o 1-1000000.annotated.sites.vcf
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| A genotyping pipeline implemented in a make file is available here.
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| === Filtering ===
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| Requires a set of features AND an installed copy of SVMLight.
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| vt filter NA12878.bam -i NA12878.sites.vcf -o NA12878.svm.sites.vcf --pos positive.sites.vcf --neg negative.sites.vcf
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| A filtering pipeline implemented in a make file is available here.
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| === Left Alignment ===
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| Left align indel type variants in a VCF file.
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| vt left_align -i mills.vcf -o mills.leftaligned.vcf
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| === Profile SNPs ===
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| Profile SNPs.
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| vt profile_snps -i mills.snps.sites.vcf
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| === Profile Indels ===
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| Profile indels.
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| vt profile_indels -i mills.indels.sites.vcf
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| === Profile MNPs ===
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| Profile MNPs.
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| vt profile_mnps -i mills.mnps.sites.vcf
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| === Sort ===
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| Sort variants according to contig lists in header.
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| vt sort -i mills.sites.vcf
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| === Split by variant ===
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| Split VCF files by variant type.
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| vt split_by_variant -i mills.sites.vcf
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| === Compute Feature ===
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| Compute feature of variant.
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| vt compute_feature -i mills.vcf
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| === Summarize Variants ===
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| Summarizes variants present in VCF file.
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| vt peek -i mills.vcf
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| === Plot Type ===
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| Plot based on type.
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| vt plot_<type> -i mills.xml
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| vt plot_<type> -i mills.xml,hgdp.xml,um.xml
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| === Resource Files ===
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| dbSNP
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| OMNI 1000G
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| Mills
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| HAPMAP
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