adjust-mods for skipped reads

[ekushele]

Hello,

I'm trying to use modkit adjust-mods on a bam file. This bam includes supplementary mapping and optical duplicates reads. It seems like the adjust-mods skip those reads. Is there an option to adjust mods also for those skipped reads?

Thank you!

[ArtRand]

Hello @ekushele,

Using secondary, supplementary, and duplicate alignments in adjust-mods is supported as long as the alignments have valid MN tags. These tags are required to properly evaluate the modified base information. Please see the documentation for more information on how to get the MN tags in your alignments.