I want to do variant calling on .bam files from Hifi data, using deepvariant. When I put .bam files that have followed the isoseq workflow to the refine step (.corrected.bam) deepvariant works, but the .bam made by groupdedup seems to remove the quality scores and wont run through deepvariant. Is groupdedup only used for isoform detection?
armintoepfer
commented
1 month ago
I want to do variant calling on .bam files from Hifi data, using deepvariant. When I put .bam files that have followed the isoseq workflow to the refine step (.corrected.bam) deepvariant works, but the .bam made by groupdedup seems to remove the quality scores and wont run through deepvariant. Is groupdedup only used for isoform detection?