This may be a naive question, but I was trying to figure out whether I should set "REMOVE_DUPLICATES" to true or false when using picard's "MarkDuplicates" to remove duplicate reads. Since I want to subsequently call variants using samtools pileup, I am not sure whether samtools pileup will then remove from consideration these duplicate reads that are marked by flags when it calls SNPs.
By setting the "REMOVE_DUPLICATES=true", my understanding is that the duplicates read will not even be written to the output file, which sounds a bit safer ...
Thanks for any insight on this!
By setting the "REMOVE_DUPLICATES=true", my understanding is that the duplicates read will not even be written to the output file, which sounds a bit safer ...
Thanks for any insight on this!
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