It looks like you're new here. If you want to get involved, click one of these buttons!
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 \
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?