Entering edit mode
10 weeks ago
brandnewatthis • 0
I am trying to filter my variants through the following parameters using GATK:
--filter-expression "QD < 2.0 || SOR > 3.0 || FS > 55.0 || MQ < 40.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0"
However, after annotating as PASS/FAIL, I have 0 passing variants. I am not sure if my parameters are too strict, or if the GATK error "unidentified variable MQRankSum" is causing this?
try again without MQRankSum ...
I ended up realizing it was a problem with bcftools - I didn't put my bgzip my vcf files therefore it couldn't read it. It looks to be fixed now, but I did end up omitting MQRankSum in case. Thank you!