I'm trying to filter for UMI<>alignment events that may be artifactual due to PCR template switching during sample prep. Currently, i filter alignments that only have 1 read at the specific site, but after UMI deduplication I cannot really do that (since one UMI does not mean one read). is there any way to do that either during the "dedup" command, or by pulling some metadata when looking at the deduplicated BAM file?
Hi!
I'm trying to filter for UMI<>alignment events that may be artifactual due to PCR template switching during sample prep. Currently, i filter alignments that only have 1 read at the specific site, but after UMI deduplication I cannot really do that (since one UMI does not mean one read). is there any way to do that either during the "dedup" command, or by pulling some metadata when looking at the deduplicated BAM file?