Genome Variant Analysis

java -jar GenomeAnalysisTK.jar
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
java -jar GenomeAnalysisTK.jar
Function: Build a recalibration model to score variant quality for filtering purposes
Usage: java -Xmx4g -jar GenomeAnalysisTK.jar -T VariantRecalibrator -R reference.fasta -input raw_variants.withASannotations.vcf -AS -resource:hapmap,known=false,training=true,truth=true,prior=15.0 hapmap_3.3.b37.sites.vcf -resource:omni,known=false,training=true,truth=false,prior=12.0 1000G_omni2.5.b37.sites.vcf -resource:1000G,known=false,training=true,truth=false,prior=10.0 1000G_phase1.snps.high_confidence.vcf -resource:dbsnp,known=true,training=false,truth=false,prior=2.0 dbsnp_135.b37.vcf -an QD -an MQ -an MQRankSum -an ReadPosRankSum -an FS -an SOR -an InbreedingCoeff -mode SNP -recalFile output.AS.recal -tranchesFile output.AS.tranches -rscriptFile output.plots.AS.R
java -jar GenomeAnalysisTK.jar
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
java -jar GenomeAnalysisTK.jar
Function: Assess sequence coverage by a wide array of metrics, partitioned by sample, read group, or library
Usage: java -jar GenomeAnalysisTK.jar -T DepthOfCoverage -R reference.fasta -o file_name_base -I input_bams.list [-geneList refSeq.sorted.txt] [-pt readgroup] [-ct 4 -ct 6 -ct 10] [-L my_capture_genes.interval_list]
java -jar GenomeAnalysisTK.jar
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
java -jar GenomeAnalysisTK.jar
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
java -jar GenomeAnalysisTK.jar
Function: Collect statistics on callable, uncallable, poorly mapped, and other parts of the genome
Usage: java -jar GenomeAnalysisTK.jar -T CallableLoci -R reference.fasta -I myreads.bam -summary table.txt -o callable_status.bed
java -jar GenomeAnalysisTK.jar
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
java -jar GenomeAnalysisTK.jar
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
java -jar GenomeAnalysisTK.jar
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
java -jar GenomeAnalysisTK.jar
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
java -jar GenomeAnalysisTK.jar
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
java -jar GenomeAnalysisTK.jar
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
java -jar GenomeAnalysisTK.jar
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
java -jar GenomeAnalysisTK.jar
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