We've moved!
This site is now read-only. You can find our new documentation site and support forum for posting questions here.
Be sure to read our welcome blog!

MarkIlluminaAdapters - why does it only accept query-sorted BAM files?

Hi, MarkIlluminaAdapters only accepts query-sorted BAM files. This limitation shouldn't exist because there are many times where one might want to analyze a coordinate sorted BAM file for Illumina adapter content. There's no reason the exact same code couldn't run on any sorted or unsorted BAM. Illumina adapters are analyzed one read at a time...


Sign In or Register to comment.