No Passing Variants GATK
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?
• 1,098 views
•
link
updated
by
Ram
•
written
by
brandnewatthis •
•
written
by
brandnewatthis •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
how to convert whole genome sequencing datasets to use for GWAS
written by ngseq •
-
gatk Hardfilter Error
written by bestone •
-
Critical criteria for filtering variants by VariantFiltration
written by Alireza •
-
Which GATK tool should I use? - VariantFiltration exomeseq
written by wiki97 •
-
Suggest vcf filtered parameter for gatk VariantFiltration
written by Mbillah
-
GATK filtering console error
written by rbioinfo •
-
GATK VariantFiltration invalid expression
written by ciemanek
-
GATK - gene panel VCF - too many variants - how to filter out
written by stanedav •
-
Question about GATK hardfiltering conditions
written by bitpir
-
Applying hard filters for variants
written by bioinforesearchquestions
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!