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