No Passing Variants GATK

Question

[brandnewatthis]

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?

[Pierre Lindenbaum]

, or if the GATK error "unidentified variable MQRankSum" is causing this

try again without MQRankSum ...

[brandnewatthis]

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!