The Frontline Support team will be offline February 18 for President's Day but will be back February 19th. Thank you for your patience as we get to all of your questions!
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