when calling variants on pooled samples, is removing duplicates recommended?

I was planning to call variants on my pooled bacteria sample using GATK UnifiedGenotyper and was wondering if removing duplicates should be in the best practices since with pooled samples, the reads might not be PCR duplicates but actually reads from different strains that I have in the pool. I would appreciate any input from your side. Thank you

Eva

Best Answers

Answers

Sign In or Register to comment.