Are duplicated records in BAM file counted or not?

broadinstitute / ichorCNA

Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing.

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Are duplicated records in BAM file counted or not? #118

Open zztin opened 1 year ago

zztin commented 1 year ago

Hi, I am wondering if ichorCNA (actually readCounter in HMMcopy) count the records in bam files if they contains flag indicating they are (PCR or optical) duplicated record (flag 0x400) by picard (MarkDuplicates)? In theory I suppose it should not count these molecules, however, I could not find clear documentation if this check is implemented or not. Could you point me to the correct forum, or perhaps you have a clue to this? Thank you very much!

ilykos commented 7 months ago

@zztin I took the liberty of replicating your question in the readCounter repository. HMMCopyUtils Issue 15. As ichorCNA works on downstream .wig files, I do not believe it has any awareness of the 0x400 flag.