Can I use UnifiedGenotyper to call somatic variants in tumor/control tissues?
Posted in Ask the GATK team | Last updated on 2013-03-28 08:09:56

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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

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