Genome Variant Analysis

Function: Splits reads that contain Ns in their CIGAR string

Usage: java -jar GenomeAnalysisTK.jar -T SplitNCigarReads -R reference.fasta -I input.bam -o output.bam -U ALLOW_N_CIGARS

Function: Select a subset of variants from a larger callset

Usage: java -jar GenomeAnalysisTK.jar -T SelectVariants -R reference.fasta -V input.vcf -o output.vcf -sn SAMPLE_1_ACTG -env -noTrim

Function: Select a subset of variants from a larger callset

Usage: java -jar GenomeAnalysisTK.jar -R ref.fasta -T SelectVariants --variant input.vcf -o output.vcf -IDs fileKeep -excludeIDs fileExclude

Function: Calculate genotype posterior likelihoods given panel data

Usage: java -jar GenomeAnalysisTK.jar -T CalculateGenotypePosteriors -R reference.fasta -supporting external.panel.vcf -V input.vcf -o output.withPosteriors.vcf --numRefSamplesIfNoCall 100

Function: Compute the most likely genotype combination and phasing for trios and parent/child pairs

Usage: java -jar GenomeAnalysisTK.jar -T PhaseByTransmission -R reference.fasta -V input.vcf -ped input.ped -o output.vcf

Function: Create a subset of a FASTA reference sequence

Usage: java -jar GenomeAnalysisTK.jar -T FastaReferenceMaker -R reference.fasta -o output.fasta -L input.intervals

Function: Select a subset of variants from a larger callset

Usage: java -jar GenomeAnalysisTK.jar -R ref.fasta -T SelectVariants -R reference.fasta -V input.vcf -o output.vcf -selectType INDEL --minIndelSize 2 --maxIndelSize 5

Function: Select a subset of variants from a larger callset

Usage: java -jar GenomeAnalysisTK.jar -T SelectVariants -R reference.fasta -V input.vcf -o output.vcf -selectType SNP -selectType MNP -restrictAllelesTo MULTIALLELIC

Function: Select a subset of variants from a larger callset

Usage: java -jar GenomeAnalysisTK.jar -T SelectVariants -R reference.fasta -V input.vcf -o output.vcf -L /path/to/my.interval_list -sn SAMPLE_1_ACTG

Function: Calculate genotype posterior likelihoods given panel data

Usage: java -jar GenomeAnalysisTK.jar -T CalculateGenotypePosteriors -R reference.fasta -V input.vcf -o output.withPosteriors.vcf --ignoreInputSamples

Function: Apply a score cutoff to filter variants based on a recalibration table

Usage: java -jar GenomeAnalysisTK.jar -T ApplyRecalibration -R reference.fasta -input raw_variants.withASannotations.vcf -AS --ts_filter_level 99.0 -tranchesFile output.AS.tranches -recalFile output.AS.recal -mode SNP -o path/to/output.recalibrated.ASfiltered.vcf

Function: Calculate genotype posterior likelihoods given panel data

Usage: java -jar GenomeAnalysisTK.jar -T CalculateGenotypePosteriors -R reference.fasta -V input.vcf --skipPopulationPriors -ped family.ped -o output.withPosteriors.vcf

Function: Estimate cross-sample contamination

Usage: java -jar GenomeAnalysisTK.jar -T ContEst -R reference.fasta -I tumor.bam --genotypes normalGenotypes.vcf --popFile populationAlleleFrequencies.vcf -L populationSites.interval_list [-L targets.interval_list] -isr INTERSECTION -o output.txt

Function: Select a subset of variants from a larger callset

Usage: java -jar GenomeAnalysisTK.jar -T SelectVariants -R reference.fasta -V myCalls.vcf --concordance theirCalls.vcf -o output.vcf -sn mySample

Function: Select a subset of variants from a larger callset

Usage: java -jar GenomeAnalysisTK.jar -T SelectVariants -R reference.fasta -V input.vcf -ped family.ped -mv -mvq 50 -o violations.vcf