How to reveal why reads are filtered out when using PrintReads?
when exploring gatk v4.beta.5-36 with
PrintReads -I foo.bam -O bar.bam, all my alignments are filtered away:
15:57:37.096 INFO PrintReads - 15201761 read(s) filtered by: WellformedReadFilter
Is there a way to get a more informative summary here, indicating why my alignments are not well formed according to
I've already digged into the sources of
org.broadinstitute.hellbender.engine.filters.CountingReadFilter (which seems to be the filter backend of PrintReads) but it does not seems to keep track of per filter statistics.
Next I'd like to disable the filter that's causing all my alignments to be filtered away, and I've noticed that I could disable individual filters with
--disableReadFilter but the docs don't seem to state what values are possible here. Where could I find a list of options without digging through the source code?
I'm rather new to gatk so thank you for your patience.