Open LeilyR opened 1 month ago
OK I found the bug, it is coming from here Filtering is only defined for bowtie2 not others. I will fix it in my locally installed one. Shall I send you a PR too?
I reopened this, since it is actually a bug to be fixed. Noticed that I cannot set a label anymore :P so maybe one of you can take care of that.
Hey Leily,
thanks for posting that issue. I've been mostly testing on bowtie2 which is the default aligner, but I agree we should fix that. I'm only aware that UMI deduplication only works for bowtie2 sofar, this is also to be fixed for other aligners.
Were you able to open a PR?
Hi, even though I set
dedup
andmapq
and see the string in thefilter_rules
, filtered bams areln -s
of the bam files. I had a quick look at the rule, but I could not easily spot an obvious issue there. Did you notice this before? I am using bwa-mem2 btw