GATK variantFiltration unexpected behaviour?

Question

[jtwalker]

Hello,

I'm trying to use the GATK to hard filter variants (I'm using a non-model organism, so variant re calibration isn't possible), but, while I'm following the GATK website's tutorial (https://gatkforums.broadinstitute.org/gatk/discussion/2806/howto-apply-hard-filters-to-a-call-set), I haven't actually been able to filter out any variants.

As an example, after subsetting out the SNP's in my GenotypeGVCFs produced VCF file, I used

gatk -T VariantFiltration -R /PATH/reference_genome -V myfile.vcf  --filterExpression "MQ>20" --filterName "mq20_filter"  -o my_filtered_file.vcf

which should have flagged any variants with mapping quality below 20 with FILTER rather than PASS. When I use grep to check if this worked in the way that I expected, I found many instances where MQ=10.

There seems to be something missing with my JEXL expression that I'm simply not seeing in the tutorial, or other GATK documentation. Can anyone help me out?

Thanks!

edit: fixed a minor mistake

[Pierre Lindenbaum]

show us a line in the VCF failing the expression, and, in the header, the line for ##INFO=<ID=MQ... please.

[jtwalker]

A line from the VCF:

NC_024218.1 10250670    .   C   T   61.23   PASS    AC=2;AF=0.333;AN=6;DP=75;ExcessHet=1.0474;FS=0.000;MLEAC=2;MLEAF=0.333;MQ=10.95;QD=30.62;SOR=0.693  GT:AD:DP:GQ:PGT:PID:PL  0/0:6,0:6:18:.:.:0,18,230   ./.:1,0:1:.:.:.:0,0,0   1/1:0,2:2:6:1|1:10250670_C_T:90,6,0 ./.:2,0:2:.:.:.:0,0,0   ./.:10,0:10:.:.:.:0,0,0 ./.:0,0:0:.:.:.:0,0,0   ./.:1,0:1:.:.:.:0,0,0   ./.:17,0:17:.:.:.:0,0,0 ./.:9,0:9:.:.:.:0,0,0   0/0:9,0:9:0:.:.:0,0,258 ./.:0,0:0:.:.:.:0,0,0   ./.:2,0:2:.:.:.:0,0,0   ./.:2,0:2:.:.:.:0,0,0   ./.:1,0:1:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0   ./.:13,0:13:.:.:.:0,0,0

and I'm not quite sure what you mean by a line from the header, but I grepped your example and what returned was this:

##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">

Thanks!

[serpalma.v]

I've encountered the same issue. Could you please provide your solution if you were able to fix this problem?

Answer 1

[andrew.j.skelton73]

Isn't there a syntax problem here? I thought that GATK's filter expressions couldn't take integers, and they needed doubles, otherwise it'd throw an error.

It should be:

--filterExpression "MQ > 20.0"

[jtwalker]

It didn't give me an error, but I'll try that now. Thanks!