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Vt (view source)

Revision as of 16:17, 21 October 2013

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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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  binaries
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  /net/fantasia/home/atks/programs/vt
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  test data
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  /net/fantasia/home/atks/programs/vt/test
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  scripts
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  /net/fantasia/home/atks/programs/vt/scripts
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External usage
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  download from sourceforge/github
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== Common options patterns ==
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    -i defines the input file and by default, this is a require parameter,
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      however, you may set it as '-' to accept STDIN which by default is
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      assumed to be a non compressed format. 
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    -o defines the out file which and has the STDOUT set as the default.
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      You may modify the STDOUT to output the binary version of the format,
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      e.g. BCF. with the option -c
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== Major Workflows ==
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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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Normalize(including left aligning) variants.  This is required as left alignment of insertions and/or deletions within a read is sometimes insufficient to ensure complete left alignment.
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vt normalize -i NA12878.bam -o NA12878.normalized.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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== Generation ==
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=== Discovery ===
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Discovers variants from bams.
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  Options:
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  -b,  --input-bam-file    : Input BAM file
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  -o,  --output-vcf-file  : Output VCF file
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  -v,  --variant-type      : Variant Types, takes on any combinations of
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                              the values snps,mnps,indels comma delimited
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                              [snps,mnps,indels]
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  -q,  --q-cutoff          : BASE Cutoff, only bases with
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                              QUAL/BAQ >= baseq are considered [13]
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  -m,  --mapq-cutoff      : MAPQ Cutoff, only alignments with
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                              map quality >= mapq are considered [20]
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  -g,  --genome-fa-file    : Genome FASTA file
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  -s,  --sample-id        : Sample ID
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  Example:
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  e.g. vt discover -b in.bam -o - -g ref.fa -v snps,indels -s HG0001
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  e.g. bam mergeBam --in a.bam --in b.bam -o - |
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        vt discover -b - -o out.sites.vcf -g ref.fa -v all -s HG0001 |
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        vt left_align -i - | vt merge_duplicate_variants
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=== Genotyping ===
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Genotypes variants for each sample.
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  Options:
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  -b,  --input-bam-file        : Input BAM file
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  -i,  --input-candidate-vcf  : Input Candidate VCF file
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  -o,  --output-vcf-file      : Output VCF file
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  -v,  --variant-type          : Variant Types, takes on any combinations
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                                  of the values snps,mnps,indels comma
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                                  delimited [snps,mnps,indels]
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  -g,  --genome-fa-file        : Genome FASTA file
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  -s,  --sample-id            : Sample ID
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  Example:
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  e.g. vt genotype -b in.bam -i candidate.sites.vcf -o - -g ref.fa -s HG0001
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== Annotation ==
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=== Make Probes ===
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Populates the info field with REFPROBE, ALTPROBE and PLEN tags for genotyping.
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  Options:
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  -i,  --input-vcf <string>      : Input VCF file
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  -o,  --output-vcf <string>    : Output VCF file [-]
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  -g,  --genome-fa              : Genome FASTA file [/net/fantasia/home/atks/ref/genome/human.g1k.v37.fa]
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  -f,  --flank-length <integer>  : Minimum Flank Length [20]
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  Example:
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  e.g. vt make_probes -i 8904indels.dups.genotypes.vcf -o probes.sites.vcf -g ref.fa
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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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=== Compute Allele balance ===
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Compute [http://genome.sph.umich.edu/wiki/Genotype_Likelihood_Based_Allele_Balance allele balance].  Outputs allele balance, allele frequency, genotype frequency.
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vt compute_ab -i mills.vcf
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=== Compute Allele Frequency ===
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Compute [http://genome.sph.umich.edu/wiki/Genotype_Likelihood_based_Allele_Frequency allele frequency].  Outputs  allele frequency and genotype frequency.
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vt compute_af -i mills.vcf
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=== Compute Inbreeding Coefficient ===
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Compute [http://genome.sph.umich.edu/wiki/Genotype_Likelihood_based_Inbreeding_Coefficient inbreeding coefficient].  Outputs inbreeding coefficient based on genotype likelihoods.
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vt compute_fic -i mills.vcf
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=== Compute HWE ===
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Compute [http://genome.sph.umich.edu/wiki/Genotype_Likelihood_based_Hardy-Weinberg_Test Hardy-Weinberg equilibrium statistic].  Outputs  PHRED scaled HWE Test p-values for biallelic as well as multiallelic variants.
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vt compute_hwe -i mills.vcf
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=== Compute Mendelian Error ===
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Compute mendelian error  statistics.  Outputs  allele frequency and genotype frequency.
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vt compute_mendel -i mills.vcf
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=== Compute features ===
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vt compute_<feature1>_<feature2>_ ... _<feature n> -i mills.vcf
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== Modification ==
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=== Left Alignment ===
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[http://genome.sph.umich.edu/wiki/Variant_Normalization Left aligns] indel type variants in a VCF file.  This differs from normalization in that it only left aligns and left trims a variant.  This affects Indels only.
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vt left_align -i mills.vcf -o mills.leftaligned.vcf
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=== Normalization ===
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[http://genome.sph.umich.edu/wiki/Variant_Normalization Normalize] variants in a VCF file.
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vt normalize -i mills.vcf -o mills.normalized.vcf
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=== Merge duplicate variants ===
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Merges duplicate variants by position with the option of considering alleles.  (This just discards the duplicate variant that appears later in the VCF file)
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  Options:
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  -i,  --input-vcf <string>  : Input VCF file
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  -o,  --output-vcf <string> : Output VCF file [-]
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  -p,  --merge-by-position  : Merge by position [false]
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  Example:
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  e.g. vt merge_duplicate_variants -i 8904indels.dups.genotypes.vcf -o out.vcf
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  e.g. vt merge_duplicate_variants -p -i 8904indels.dups.genotypes.vcf -o out.vcf
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== Profiling ==
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A standard procedure is as follows:
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  zcat dataset.vcf.gx | vt normalize -i - | vt merge_duplicate_variants -i - > dataset.normalized.vcf
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  cut -f1-8 dataset.normalized.vcf > dataset.sites.vcf
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  cat dataset.normalized.sites.vcf | vt profile_snps -i - > snps.summary.log
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=== Profile SNPs ===
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Profile SNPs.
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* ts/tv ratio
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* overlap analyses
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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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* Overlap analyses with known data sets
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* FS/NFS annotation
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vt profile_indels 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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=== 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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== Plotting ==
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=== Allele Frequency Spectrum ===
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Plots Allele Frequency Spectrum of variants found in VCF file
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vt plot_afs -i mills.xml
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=== Genotype Likelihood Concordance ===
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Plots Genotype Likelihood Concordance graph.
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vt plot_gl -i mills.xml
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=== Allele Balance Spectrum===
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Plots Allele Balance graph of variants in the VCF file.
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vt plot_ab -i mills.xml
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= VCF File Manipulation =
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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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= 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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= Maintained by =
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This page is maintained by  [mailto:atks@umich.edu Adrian]
Atks
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Retrieved from "http://genome.sph.umich.edu/wiki/Special:MobileDiff/8869"

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