Can I use UnifiedGenotyper to call somatic variants in tumor/control tissues?

I067569I067569 Posts: 0Member
edited March 2013 in Ask the GATK team


I am interested in the following scenario: 1. sequence tumor and control samples to separate fastq files. 2. Execute read alignment for the 2 samples separately. 3. Execute UnifiedGenotyper with the 2 BAM files (control and tumor) with the following command:

java -jar GenomeAnalysisTK.jar \ -T UnifiedGenotyper \ -R ReferenceGenome.fasta \ -I contro.bam -I tumor.bam \ -D /usr/sap/GenomicsPlatform/dbSNP/dbsnp_137.b37.vcf \ -o output.vcf

Is this a proper usage for UnifiedGenotyper? How does UnifiedGenotyper refer to the 2 BAM files it recieves as input? What do I expect to see in the output.vcf file? are they somatic variants which describe the variation between control and tumor samples?

Thank you, Stas

Post edited by I067569 on

Best Answer


Sign In or Register to comment.