Open will-NYGC opened 7 years ago
Hi, I thought I'd bump this since I'm still having issues. I've tried running biscuit markdup infile.bam out.file.bam
on my data for a couple of different aligned BAMs and keep getting the above error. They're BWA-meth aligned so should work. Have you seen this issue before?
Hi Will, Thanks for reporting. This is a bug with the bam header. See if the following solved the problem. release.zip I will include the change in the new release.
Wanding
looks to be fixed. thanks, wanding!
nb. I find that I have to re-sort the markdup'ed BAM in order to index it and proceed with pileup'ing.
I'm testing out your pipeline and am getting an error on BAM files produced after running
biscuit markdups
.[E::bam_hdr_read] invalid BAM binary header
Further, progress output suggests no dups are marked although dup rates based on picard MarkDuplicates are in the order of 20%.
do you know why my BAM header is invalid? related to stderr suggesting no dups marked?