Genome Variant Analysis

java -jar GenomeAnalysisTK.jar
Function: Call germline SNPs and indels via local re-assembly of haplotypes
Usage: 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
java -jar GenomeAnalysisTK.jar
Function: Call germline SNPs and indels via local re-assembly of haplotypes
Usage: 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
java -jar GenomeAnalysisTK.jar
Function: Validate a VCF file with an extra strict set of criteria
Usage: java -jar GenomeAnalysisTK.jar -T ValidateVariants -R reference.fasta -V input.vcf --dbsnp dbsnp.vcf --reference_window_stop 208
java -jar GenomeAnalysisTK.jar
Function: Call somatic SNPs and indels via local re-assembly of haplotypes
Usage: java -jar GenomeAnalysisTK.jar -T CombineVariants -R reference.fasta -V output.normal1.vcf -V output.normal2.vcf [-V output.normal2.vcf ...] -minN 2 --setKey "null" --filteredAreUncalled --filteredrecordsmergetype KEEP_IF_ANY_UNFILTERED [-L targets.interval_list] -o MuTect2_PON.vcf
java -jar GenomeAnalysisTK.jar
Function: 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.
Usage: java -cp GenomeAnalysisTK.jar org.broadinstitute.gatk.tools.GatherBqsrReports -I input.list -O output.grp
java -jar GenomeAnalysisTK.jar
Function: Call somatic SNPs and indels via local re-assembly of haplotypes
Usage: java -jar GenomeAnalysisTK.jar -T MuTect2 -R reference.fasta -I:tumor normal1.bam [--dbsnp dbSNP.vcf] [--cosmic COSMIC.vcf] --artifact_detection_mode [-L targets.interval_list] -o output.normal1.vcf
java -jar GenomeAnalysisTK.jar
Function: Call germline SNPs and indels via local re-assembly of haplotypes
Usage: 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
java -jar GenomeAnalysisTK.jar
Function: Call somatic SNPs and indels via local re-assembly of haplotypes
Usage: 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
VarScan
Function: Call variants and identifies their somatic status (Germline/LOH/Somatic) using pileup files from a matched tumor-normal pair
Usage: java -jar VarScan.jar somatic [normal_pileup] [tumor_pileup] [output] OPTIONS
SnpEff
Function: This tool calculate the effect of variants (SNPs/MNPs/Insertions) and deletions.
Usage: java -jar snpEff.jar
java -jar GenomeAnalysisTK.jar
Function: Perform local realignment of reads around indels
Usage: java -jar GenomeAnalysisTK.jar -T IndelRealigner -R reference.fasta -I input.bam -known indels.vcf -targetIntervals intervalListFromRTC.intervals -o realignedBam.bam
VarScan
Function: Limits variants in a file to a set of positions or regions
Usage: java -jar VarScan.jar limit [infile] OPTIONS
java -jar GenomeAnalysisTK.jar
Function: Call germline SNPs and indels via local re-assembly of haplotypes
Usage: java -jar GenomeAnalysisTK.jar -R reference.fasta -T HaplotypeCaller -I sample1.bam --emitRefConfidence GVCF [--dbsnp dbSNP.vcf] [-L targets.interval_list] -G Standard -G AS_Standard -o output.raw.snps.indels.AS.g.vcf
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 --setFilteredGtToNocall
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