gatk v4.14.0 does not recognize matematical operators

Question

[dago]

Dear all I have problem with filtering the SNPs called with gatk v4.1.4.0. I have a vcf file that looks like this:

    contig00001     8227    .       A       G       40.68   .       AC=1;AF=0.100;AN=10;BaseQRankSum=-0.861;ClippingRankSum=0.000;DP=88;FS=13.035;MLEAC=1;MLEAF=0.100;MQ=60.00;MQRankSum=0.000;QD=0.46;ReadPosRankSum=-0.300;SOR=2.792      GT:AD:DP:GQ:PL  0/0/0/0/0/0/0/0/0/1:85,3:88:34:66,0,34,78,132,196,276,380,528,782,6199
    contig00001     8244    .       T       C       43.68   .       AC=1;AF=0.100;AN=10;BaseQRankSum=-0.838;ClippingRankSum=0.000;DP=80;FS=15.529;MLEAC=1;MLEAF=0.100;MQ=60.00;MQRankSum=0.000;QD=0.55;ReadPosRankSum=-1.716;SOR=2.783      GT:AD:DP:GQ:PL  0/0/0/0/0/0/0/0/0/1:77,3:80:31:69,0,31,71,119,178,251,347,482,716,5872
    contig00001     8846    .       C       T       72.68   .       AC=1;AF=0.100;AN=10;BaseQRankSum=0.659;ClippingRankSum=0.000;DP=88;FS=2.385;MLEAC=1;MLEAF=0.100;MQ=59.93;MQRankSum=0.273;QD=0.83;ReadPosRankSum=-4.696;SOR=1.102        GT:AD:DP:GQ:PL  0/0/0/0/0/0/0/0/0/1:84,4:88:31:98,0,31,72,124,186,264,366,510,759,3392
    contig00001     9854    .       A       G       42.69   .       AC=1;AF=0.100;AN=10;BaseQRankSum=0.463;ClippingRankSum=0.000;DP=79;FS=11.687;MLEAC=1;MLEAF=0.100;MQ=60.00;MQRankSum=0.000;QD=0.55;ReadPosRankSum=1.267;SOR=2.799        GT:AD:DP:GQ:PL  0/0/0/0/0/0/0/0/0/1:74,3:77:29:68,0,29,66,111,166,235,324,450,665,2970
    contig00001     19796   .       A       G       34.70   .       AC=1;AF=0.100;AN=10;BaseQRankSum=-2.543;ClippingRankSum=0.000;DP=66;FS=10.825;MLEAC=1;MLEAF=0.100;MQ=60.00;MQRankSum=0.000;QD=0.53;ReadPosRankSum=-0.600;SOR=0.829      GT:AD:DP:GQ:PL  0/0/0/0/0/0/0/0/0/1:63,3:66:23:60,0,23,54,93,140,199,275,384,572,2745
    contig00001     20699   .       T       C       47.70   .       AC=1;AF=0.100;AN=10;BaseQRankSum=0.326;ClippingRankSum=0.000;DP=66;FS=2.442;MLEAC=1;MLEAF=0.1

I would like to filter the SNPs now, e.g. gatk VariantFiltration -V GenomeA.rawSNPs.vcf -filter "QD < 2" --filter-name "snp_def" -O test.vcf

or

gatk VariantFiltration -R ../GenomeA_contigs.fa -V GenomeA.rawSNPs.vcf -O test.vcf --filter-name "snp" --filter-expression "MQ < 60.0"

However, I keep getting the following error:

A USER ERROR has occurred: Invalid argument '<'.

I believe there is a problem in recognizing the mathematical operators or with "/' I tried various combionation with or without "/' but I am still getting the same error. I cannto quite figure out where the problem is. Can you guys spot the problem?

Thank you

[dago]

I also posted this issue on the gatk github, sorry for the double posting

Answer 1

[Mark]

I think the syntax is --filter-name then -filter. You specify filter first then the filter name.

See the documentation here: https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_hellbender_tools_walkers_filters_VariantFiltration.php

[dago]

Thanks for your comment. I jsut tried and it gives me the same error.

[Mark]

Oh! you're missing the reference sequence so include -R seq.fa at the start. Follow the manual precisely. I think the order of flag input is very important (and spaces too).

[dago]

Sorry, I did that as well, but I still get the same error. I edit my post now

[Mark]

Okay this is the last thing I can think of. Try matching exactly the type of values. In the first example you gave QD is a float so make sure its "QD < 2.0" and in the second MQ is two decimals (shoudn't make a diff but try) MQ < 60.00. I didn't think MQ was a float I thought it was an int so its weird to see it as a float in your file. Not sure whats happening

See the caveats mentioned here: https://software.broadinstitute.org/gatk/documentation/article.php?id=1255

[dago]

Thank you @Amar, I appreciate your suggestions. I tried what you said as well 20.0, 20, 20.00. Always the same. I personally believe that there is an issue with Java.

[fireprophet.io]

Hello, dago! If you finally solve this problem could you share how you fix it?