Picard MarkDuplicates tool on a pooled sample BAM

Question

[joneill4x]

Would the Picard MarkDuplicates tool be acceptable to use on a pooled sample BAM file? (Multiple diploid samples have their DNA extracted, the DNA is pooled together, then the pool of DNA is sequenced) Or is it meant only for a single diploid sample?

Thank you.

[Ram]

"pooled" samples and "diploid" samples are not mutually exclusive or even comparable concepts. "Diploid" refers to the number of sets of chromosomes in the organism, whereas "pooled" samples is a concept from experiment design during sequencing or downstream analysis.

[joneill4x]

Sorry, my mistake. I meant to ask: Would the Picard MarkDuplicates tool be acceptable to use on a pooled sample BAM file?(Multiple diploid samples have their DNA extracted, the DNA is pooled together, then the pool of DNA is sequenced). Or is it meant only for a single diploid sample?

[ATpoint]

It does not matter how the library was made. The tool will remove sequences with identical mapping positions. There is no way to distinguish true PCR replicates from identical fragments that come from different samples prior to pooling. Typically duplicates are marked prior to any downstream application in DNA-seq.