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tumor cohort versus normal cohort variation comparison
Dear GATK group,
We aim to compare snp/indel differences between a tumor cohort and a normal cohort. Going through your documents, we see GATK tumor/normal pair branch, which seems to be based on one tumor sample and one corresponding normal sample. We also see cohort approach which include joint variation call step in the haplotype caller step. I am wondering how to do a tumor/normal pair approach basing on tumor cohort and normal cohort using joint variation call option across all tumor samples and across all normal samples (also realign tumor and normal samples together).
Our current approach is to merge all tumor bam files as one sample, and to merge all normal bam files as one sample, then use tumor/normal pair flow. But the cohort joint variation call across all tumor samples and all normal samples is not implemented in the merged bam files, is it right? In another word, we have to separate every tumor samples in order to perform joint variation call in the haplotypecaller step. Is it right?
Looking forward to hearing from your suggestions.