VariantFiltration warning "undefined variable"

Question

[felipead66]

When I run

./gatk VariantFiltration -R genome.fasta -V vcf_file.vcf -o outfit_vcf.vcf --filter-expression "QD <2.0" --filter-name "qdthres"

I get a warning:

undefined variable QD

The same happens when I use MQ, FS, MQRankSum

[ATpoint]

head -n 30 vcf_file.vcf ?

[felipead66]

#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  tredna_sm
gene.1  1039    .   C   T   107.77  .   AC=1;AF=0.500;AN=2;BaseQRankSum=1.293;DP=40;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=51.55;MQRankSum=-3.589;QD=2.76;ReadPosRankSum=0.097;SOR=0.446  GT:AD:DP:GQ:PL  0/1:33,6:39:99:136,0,4437
gene.1  1064    .   G   A   91.77   .   AC=1;AF=0.500;AN=2;BaseQRankSum=-1.172;DP=34;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=51.01;MQRankSum=-3.701;QD=2.70;ReadPosRankSum=1.727;SOR=0.977 GT:AD:DP:GQ:PL  0/1:29,5:34:99:120,0,5668
gene.1  1067    .   A   G   94.77   .   AC=1;AF=0.500;AN=2;BaseQRankSum=-0.241;DP=33;ExcessHet=3.0103;FS=1.830;MLEAC=1;MLEAF=0.500;MQ=50.81;MQRankSum=-3.721;QD=2.87;ReadPosRankSum=1.407;SOR=0.934 GT:AD:DP:GQ:PL  0/1:28,5:33:99:123,0,5757
gene.1  1080    .   G   A   103.77  .   AC=1;AF=0.500;AN=2;BaseQRankSum=0.030;DP=30;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=49.13;MQRankSum=-3.520;QD=3.46;ReadPosRankSum=1.030;SOR=0.971  GT:AD:DP:GQ:PL  0/1:25,5:30:99:132,0,5429
gene.1  1101    .   G   A   118.77  .   AC=1;AF=0.500;AN=2;BaseQRankSum=0.074;DP=26;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=45.80;MQRankSum=-3.299;QD=4.57;ReadPosRankSum=-1.109;SOR=0.914 GT:AD:DP:GQ:PL  0/1:21,5:26:99:147,0,4674
gene.1  1116    .   A   T   79.77   .   AC=1;AF=0.500;AN=2;BaseQRankSum=-0.970;DP=22;ExcessHet=3.0103;FS=2.643;MLEAC=1;MLEAF=0.500;MQ=41.89;MQRankSum=-1.947;QD=3.63;ReadPosRankSum=-0.576;SOR=0.966    GT:AD:DP:GQ:PL  0/1:19,3:22:99:108,0,4112
gene.1  1118    .   C   G   40.77   .   AC=1;AF=0.500;AN=2;BaseQRankSum=0.060;DP=19;ExcessHet=3.0103;FS=2.629;MLEAC=1;MLEAF=0.500;MQ=38.26;MQRankSum=-1.755;QD=2.15;ReadPosRankSum=-1.345;SOR=0.976 GT:AD:DP:GQ:PL  0/1:16,3:19:69:69,0,3907
gene.1  1125    .   G   A   11.12   .   AC=1;AF=0.500;AN=2;BaseQRankSum=1.007;DP=17;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=37.25;MQRankSum=-1.434;QD=0.65;ReadPosRankSum=-0.748;SOR=0.260 GT:AD:DP:GQ:PL  0/1:15,2:17:39:39,0,2939
gene.1  1299    .   C   T   82.77   .   AC=1;AF=0.500;AN=2;BaseQRankSum=-0.298;DP=16;ExcessHet=3.0103;FS=15.911;MLEAC=1;MLEAF=0.500;MQ=30.48;MQRankSum=-0.589;QD=5.17;ReadPosRankSum=0.341;SOR=3.589    GT:AD:DP:GQ:PL  0/1:11,5:16:99:111,0,365
gene.1  1400    .   A   C   517.77  .   AC=1;AF=0.500;AN=2;BaseQRankSum=0.873;DP=27;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=26.80;MQRankSum=-0.507;QD=19.18;ReadPosRankSum=1.053;SOR=2.066 GT:AD:DP:GQ:PL  0/1:7,20:27:99:546,0,137
gene.1  1522    .   G   A   1158.77 .   AC=1;AF=0.500;AN=2;BaseQRankSum=1.529;DP=91;ExcessHet=3.0103;FS=31.227;MLEAC=1;MLEAF=0.500;MQ=36.96;MQRankSum=-2.404;QD=12.73;ReadPosRankSum=0.103;SOR=1.052    GT:AD:DP:GQ:PL  0/1:48,43:91:99:1187,0,1575
gene.1  1545    .   T   C   326.77  .   AC=1;AF=0.500;AN=2;BaseQRankSum=0.459;DP=99;ExcessHet=3.0103;FS=33.072;MLEAC=1;MLEAF=0.500;MQ=37.09;MQRankSum=1.296;QD=3.30;ReadPosRankSum=-0.259;SOR=4.042 GT:AD:DP:GQ:PL  0/1:84,15:99:99:355,0,3163
gene.1  1620    .   A   G   268.77  .   AC=1;AF=0.500;AN=2;BaseQRankSum=-0.826;DP=53;ExcessHet=3.0103;FS=1.179;MLEAC=1;MLEAF=0.500;MQ=37.66;MQRankSum=-1.282;QD=5.07;ReadPosRankSum=0.642;SOR=0.982 GT:AD:DP:GQ:PL  0/1:38,15:53:99:297,0,1114
gene.1  1661    .   C   T   187.77  .   AC=1;AF=0.500;AN=2;BaseQRankSum=-1.919;DP=58;ExcessHet=3.0103;FS=1.492;MLEAC=1;MLEAF=0.500;MQ=45.31;MQRankSum=-0.928;QD=3.35;ReadPosRankSum=-0.450;SOR=1.127    GT:AD:DP:GQ:PL  0/1:44,12:56:99:216,0,1486
gene.1  1690    .   C   T   139.77  .   AC=1;AF=0.500;AN=2;BaseQRankSum=0.500;DP=64;ExcessHet=3.0103;FS=10.091;MLEAC=1;MLEAF=0.500;MQ=49.06;MQRankSum=-2.519;QD=2.37;ReadPosRankSum=-0.021;SOR=2.858    GT:AD:DP:GQ:PL  0/1:50,9:59:99:168,0,1830
gene.1  1697    .   A   C   1066.77 .   AC=1;AF=0.500;AN=2;BaseQRankSum=0.773;DP=63;ExcessHet=3.0103;FS=27.190;MLEAC=1;MLEAF=0.500;MQ=48.78;MQRankSum=-4.988;QD=19.40;ReadPosRankSum=0.453;SOR=4.203    GT:AD:DP:GQ:PL  0/1:23,32:55:99:1095,0,722
gene.1  1789    .   T   TG  362.74  .   AC=2;AF=1.00;AN=2;DP=9;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=36.64;QD=25.36;SOR=1.402 GT:AD:DP:GQ:PL  1/1:0,9:9:30:400,30,0
gene.1  1889    .   G   A   127.77  .   AC=1;AF=0.500;AN=2;BaseQRankSum=-0.137;DP=34;ExcessHet=3.0103;FS=15.431;MLEAC=1;MLEAF=0.500;MQ=51.46;MQRankSum=-3.190;QD=3.76;ReadPosRankSum=-1.811;SOR=4.039   GT:AD:DP:GQ:PL  0/1:27,7:34:99:156,0,941
gene.1  2011    .   C   T   458.77  .   AC=1;AF=0.500;AN=2;BaseQRankSum=1.415;DP=42;ExcessHet=3.0103;FS=2.885;MLEAC=1;MLEAF=0.500;MQ=51.84;MQRankSum=-2.327;QD=10.92;ReadPosRankSum=0.467;SOR=1.329 GT:AD:DP:GQ:PL  0/1:28,14:42:99:487,0,1130
gene.1  2017    .   C   A   433.77  .   AC=1;AF=0.500;AN=2;BaseQRankSum=1.007;DP=40;ExcessHet=3.0103;FS=2.919;MLEAC=1;MLEAF=0.500;MQ=52.60;MQRankSum=-2.187;QD=10.84;ReadPosRankSum=0.621;SOR=1.138 GT:AD:DP:GQ:PL  0/1:27,13:40:99:462,0,1133

[Pierre Lindenbaum]

It cannot be the 30th lines of the VCF: there is no ##INFO, no ##FORMAT etc.

[rimgubaev]

Currently facing the same problem tried GATK4 and GATK3.8: both produce the "undefined variable" for my filters. I found this forum (https://gatkforums.broadinstitute.org/gatk/discussion/2334/undefined-variable-variantfiltration) but still don't get an idea of how to deal with the problem. BTW my vcf file contains ##INFO rows in the beginning.

Answer 1

[Pierre Lindenbaum]

there is no QD in the INFO column.

[felipead66]

Actually there is, that is why I wonder

[scchess]

I had the same problem. I'm sure it was there.