[picard] MarkDuplicates.jar 에서 MAPQ should be 0 for unmapped read

Exception in thread "main" java.lang.RuntimeException: SAM validation error: ERROR: Record 62094965, Read name ILLUMINA-A16956_100211:4:14:19403:10471#0, MAPQ should be 0 for unmapped read

이러한 에러 발생시,

VALIDATION_STRINGENCY=LENIENT

옵션을 추가해준다.


This is a common problem, and you'll run into it with all the Picard suite of tools.

There's a setting that goes something like VALIDATION_STRINGENCY, and if you set it to LENIENT, it will complain about those reads, but it won't stop on them.

This happens with bwa, because it concatenates reference sequence, which leads to slightly odd things happening when a read aligns over the overlap. So this might be the source of your problem. Regardless of what's causing it, you can examine the problem reads, and cut them out, or change the stringency to let them go through.