Genome Analysis Toolkit

Variant Discovery in High-Throughput Sequencing Data

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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

FilterMutectCalls Follow

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    I want generation a bam filie in this step, so i add "--add-output-sam-program-record filtered.bam" in the end of the command,

    gatk FilterMutectCalls -R /home/dlin/reference/bwa-ref-hg19/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa -V unfiltered.vcf --tumor-segmentation segments.table --contamination-table calculatecontamination.table --ob-priors read-orientation-model.tar.gz -O filtered.vcf --add-output-sam-program-record filtered.bam

    but is dosen't work,i don't know what's wrong there.

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