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VarScan java -jar VarScan.jar limit [infile] OPTIONS This command limits variants in a file to a set of positions or regions Show
java -jar GenomeAnalysisTK.jar java -jar GenomeAnalysisTK.jar -T ValidateVariants -R reference.fasta -V input.vcf --dbsnp dbsnp.vcf --reference_window_stop 208 Validate a VCF file with an extra strict set of criteria Show
VarScan java -jar VarScan.jar somatic [normal_pileup] [tumor_pileup] [output] OPTIONS This command calls variants and identifies their somatic status (Germline/LOH/Somatic) using pileup files from a matched tumor-normal pair Show
java -jar GenomeAnalysisTK.jar java -cp GenomeAnalysisTK.jar org.broadinstitute.gatk.tools.GatherBqsrReports -I input.list -O output.grp Gather recalibration reports from parallelized base recalibration runs This tool is intended to be used to combine recalibration tables from runs of BaseRecalibrator parallelized per-interval. Show
java -jar GenomeAnalysisTK.jar java -jar GenomeAnalysisTK.jar -R reference.fasta -T HaplotypeCaller -I sample1.bam --emitRefConfidence GVCF [--dbsnp dbSNP.vcf] [-L targets.interval_list] -o output.raw.snps.indels.g.vcf Call germline SNPs and indels via local re-assembly of haplotypes Show
SnpEff java -jar snpEff.jar This tool calculate the effect of variants (SNPs/MNPs/Insertions) and deletions. Show
java -jar GenomeAnalysisTK.jar java -jar GenomeAnalysisTK.jar -T SplitNCigarReads -R reference.fasta -I input.bam -o output.bam -U ALLOW_N_CIGARS Splits reads that contain Ns in their CIGAR string Show
java -jar GenomeAnalysisTK.jar java -jar GenomeAnalysisTK.jar -R reference.fasta -T HaplotypeCaller -I sample1.bam [--dbsnp dbSNP.vcf] -stand_call_conf 20 -o output.raw.snps.indels.vcf Call germline SNPs and indels via local re-assembly of haplotypes Show
java -jar GenomeAnalysisTK.jar java -jar GenomeAnalysisTK.jar -T PhaseByTransmission -R reference.fasta -V input.vcf -ped input.ped -o output.vcf Compute the most likely genotype combination and phasing for trios and parent/child pairs Show
java -jar GenomeAnalysisTK.jar java -jar GenomeAnalysisTK.jar -T FastaReferenceMaker -R reference.fasta -o output.fasta -L input.intervals Create a subset of a FASTA reference sequence Show
java -jar GenomeAnalysisTK.jar 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 Build a recalibration model to score variant quality for filtering purposes Show
java -jar GenomeAnalysisTK.jar java -jar GenomeAnalysisTK.jar -R reference.fasta -T HaplotypeCaller -I sample1.bam [-I sample2.bam ...] [--dbsnp dbSNP.vcf] [-stand_call_conf 30] [-L targets.interval_list] -o output.raw.snps.indels.vcf Call germline SNPs and indels via local re-assembly of haplotypes Show
java -jar GenomeAnalysisTK.jar java -jar GenomeAnalysisTK.jar -T MuTect2 -R reference.fasta -I:tumor tumor.bam -I:normal normal.bam [--dbsnp dbSNP.vcf] [--cosmic COSMIC.vcf] [-L targets.interval_list] -o output.vcf Call somatic SNPs and indels via local re-assembly of haplotypes Show
java -jar GenomeAnalysisTK.jar java -jar GenomeAnalysisTK.jar -T CalculateGenotypePosteriors -R reference.fasta -V input.vcf -o output.withPosteriors.vcf --ignoreInputSamples Calculate genotype posterior likelihoods given panel data Show
java -jar GenomeAnalysisTK.jar java -jar GenomeAnalysisTK.jar -T IndelRealigner -R reference.fasta -I input.bam -known indels.vcf -targetIntervals intervalListFromRTC.intervals -o realignedBam.bam Perform local realignment of reads around indels Show
java -jar GenomeAnalysisTK.jar java -jar GenomeAnalysisTK.jar -R ref.fasta -T SelectVariants --variant input.vcf -o output.vcf -IDs fileKeep -excludeIDs fileExclude Select a subset of variants from a larger callset Show
java -jar GenomeAnalysisTK.jar java -jar GenomeAnalysisTK.jar -T CalculateGenotypePosteriors -R reference.fasta -V input.vcf --skipPopulationPriors -ped family.ped -o output.withPosteriors.vcf Calculate genotype posterior likelihoods given panel data Show
java -jar GenomeAnalysisTK.jar java -jar GenomeAnalysisTK.jar -T CalculateGenotypePosteriors -R reference.fasta -V NA12878.wgs.HC.vcf -supporting 1000G_EUR.genotypes.combined.vcf -o NA12878.wgs.HC.posteriors.vcf Calculate genotype posterior likelihoods given panel data Show
java -jar GenomeAnalysisTK.jar java -jar GenomeAnalysisTK.jar -T SelectVariants -R reference.fasta -V input.vcf -o output.vcf -sn SAMPLE_1_ACTG -env -noTrim Select a subset of variants from a larger callset Show
java -jar GenomeAnalysisTK.jar java -jar GenomeAnalysisTK.jar -T BaseRecalibrator -R reference.fasta -I my_reads.bam -knownSites latest_dbsnp.vcf -o recal_data.table Detect systematic errors in base quality scores Show