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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
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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]
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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"
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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
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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
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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]
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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
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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
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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
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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
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Function: Calculate read counts per allele for allele-specific expression analysis
Usage: java -jar GenomeAnalysisTK.jar -R reference.fasta -T ASEReadCounter -o file_name.csv -I input.bam -sites sites.vcf -U ALLOW_N_CIGAR_READS [-minDepth 10] [--minMappingQuality 10] [--minBaseQuality 2] [-drf DuplicateRead]
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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"
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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
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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
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Function: Select a subset of variants from a larger callset
Usage: java -jar GenomeAnalysisTK.jar -T SelectVariants -R reference.fasta -V hapmap.vcf --discordance myCalls.vcf -o output.vcf -sn mySample