Genome Variant Analysis

Function: Select a subset of variants from a larger callset

Usage: java -Xmx2g -jar GenomeAnalysisTK.jar -R ref.fasta -T SelectVariants -R reference.fasta -V input.vcf -o output.vcf -se 'SAMPLE.+PARC' -select "QD > 10.0"

Function: Estimate cross-sample contamination

Usage: java -jar GenomeAnalysisTK.jar -T ContEst -R reference.fasta -I:eval tumor.bam -I:genotype normal.bam --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 -R ref.fasta -T SelectVariants -R reference.fasta -V input.vcf -o output.vcf -sn SAMPLE_1_ACTG -env -ef

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 -fraction 0.5

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 -sn SAMPLE_A_PARC -sn SAMPLE_B_ACTG

Function: Concatenate VCF files of non-overlapping genome intervals, all with the same set of samples

Usage: java -cp GenomeAnalysisTK.jar org.broadinstitute.gatk.tools.CatVariants -R reference.fasta -V input1.vcf -V input2.vcf -out output.vcf -assumeSorted

Function: General-purpose tool for variant evaluation (% in dbSNP, genotype concordance, Ti/Tv ratios, and a lot more)

Usage: java -jar GenomeAnalysisTK.jar -T VariantEval -R reference.fasta -o output.eval.grp --eval:set1 set1.vcf --eval:set2 set2.vcf [--comp comp.vcf]

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

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 -invMv -o violations.vcf

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: Filter variant calls based on INFO and FORMAT annotations

Usage: java -jar GenomeAnalysisTK.jar -T VariantFiltration -R reference.fasta -o output.vcf --variant input.vcf --filterExpression "AB 50" --filterName "SomeFilterName"

Function: Detect systematic errors in base quality scores

Usage: java -jar GenomeAnalysisTK.jar -T BaseRecalibrator -R reference.fasta -I my_reads.bam -knownSites latest_dbsnp.vcf -o recal_data.table

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.vcf --ts_filter_level 99.0 -tranchesFile output.tranches -recalFile output.recal -mode SNP -o path/to/output.recalibrated.filtered.vcf

Function: Call SNPs and indels on a per-locus basis

Usage: java -jar GenomeAnalysisTK.jar -T UnifiedGenotyper -R reference.fasta -I input.bam -o raw_variants.vcf --output_mode EMIT_ALL_SITES

Function: GIREMI is a method that can identify RNA editing sites using one RNA-seq data set without requiring genome sequence data.

Usage: giremi [options] in1.bam [in2.bam [...]]