VariantFiltration ReadPosRankSum & MQRankSum undefined

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priyanka_surana

• February 20, 2020 23:45

I am using GATK version 4.1.4.1 on PBS Pro. 

Command:

gatk VariantFiltration -R ref.fa -V raw.vcf -O filtered.vcf --filter-name "QD13" --filter-expression "QD < 13.0" --filter-name "FS25" --filter-expression "FS > 25.0" --filter-name "SOR2" --filter-expression "SOR > 2.0" --filter-name "MQ59" --filter-expression "MQ < 59.0" --filter-name "MQRankSum05" --filter-expression "MQRankSum < 0.5" --filter-name "ReadPosRankSum2n" --filter-expression "ReadPosRankSum < -2.0"

Error: $ tail gatk.err

14:23:38.458 WARN  JexlEngine - ![0,14]: 'ReadPosRankSum < -2.0;' undefined variable ReadPosRankSum

14:23:38.458 WARN  JexlEngine - ![0,9]: 'MQRankSum < 0.5;' undefined variable MQRankSum

14:23:38.458 WARN  JexlEngine - ![0,14]: 'ReadPosRankSum < -2.0;' undefined variable ReadPosRankSum

14:23:38.458 WARN  JexlEngine - ![0,9]: 'MQRankSum < 0.5;' undefined variable MQRankSum

14:23:38.458 WARN  JexlEngine - ![0,14]: 'ReadPosRankSum < -2.0;' undefined variable ReadPosRankSum

14:23:38.459 INFO  ProgressMeter -       WSR196:3547035              0.0                 28629         608911.7

14:23:38.459 INFO  ProgressMeter - Traversal complete. Processed 28629 total variants in 0.0 minutes.

14:23:38.519 INFO  VariantFiltration - Shutting down engine

[February 20, 2020 2:23:38 PM AEDT] org.broadinstitute.hellbender.tools.walkers.filters.VariantFiltration done. Elapsed time: 0.06 minutes.

Runtime.totalMemory()=2453143552

Raw VCF file:

$ grep -v "^#" raw.vcf | head

WSR001 4102 . T C 690.03 . AC=2;AF=1.00;AN=2;DP=23;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=28.50;QD=30.00;SOR=1.426 GT:AD:DP:GQ:PL 1/1:0,23:23:69:704,69,0

WSR001 10596 . A G 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=30.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0

WSR001 20107 . G T 596.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.935;DP=47;ExcessHet=3.0103;FS=3.066;MLEAC=1;MLEAF=0.500;MQ=29.45;MQRankSum=0.541;QD=12.69;ReadPosRankSum=-0.288;SOR=1.426 GT:AD:DP:GQ:PL 0/1:24,23:47:99:604,0,602

WSR001 21730 . TGG T 345.09 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.593;DP=19;ExcessHet=3.0103;FS=6.532;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=28.76;ReadPosRankSum=1.593;SOR=2.788 GT:AD:DP:GQ:PL 1/1:1,11:12:20:344,20,0

WSR001 39234 . G T 61.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.000;DP=6;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=20.35;MQRankSum=-0.431;QD=10.27;ReadPosRankSum=-1.834;SOR=1.179 GT:AD:DP:GQ:PL 0/1:4,2:6:69:69,0,184

WSR001 39238 . T A 61.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.366;DP=7;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=20.30;MQRankSum=-0.366;QD=8.80;ReadPosRankSum=-0.712;SOR=0.892 GT:AD:DP:GQ:PL 0/1:5,2:7:69:69,0,184

WSR001 42502 . AGG A 39.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.096;DP=33;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=38.19;MQRankSum=-1.233;QD=1.89;ReadPosRankSum=2.778;SOR=0.693 GT:AD:DP:GQ:PL 0/1:18,3:21:47:47,0,381

WSR001 57603 . CA C 351.02 . AC=2;AF=1.00;AN=2;DP=10;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=37.98;QD=25.36;SOR=1.085 GT:AD:DP:GQ:PL 1/1:0,10:10:30:365,30,0

WSR001 60012 . T G 234.93 . AC=2;AF=1.00;AN=2;DP=6;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=36.71;QD=28.73;SOR=3.912 GT:AD:DP:GQ:PL 1/1:0,6:6:18:249,18,0

WSR001 60041 . C T 366.01 . AC=2;AF=1.00;AN=2;DP=9;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=37.84;QD=30.97;SOR=4.615 GT:AD:DP:GQ:PL 1/1:0,9:9:27:380,27,0

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• 

  cruckert

  • February 21, 2020 11:50
  • Edited

  This was already answered in the old forum:
  

   

  https://gatkforums.broadinstitute.org/gatk/discussion/8323/why-do-mqranksum-and-readposranksum-not-appear-in-some-vcf-file-entries 

  It is just a warning message.

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  Begonia_pavonina

  • August 11, 2020 11:59

  Argh, too bad the link is broken now!

  Would you have any other link to the answer?

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  Genevieve Brandt (she/her)

  • August 11, 2020 14:27

  Hi Begonia_pavonina, all of our discussions from the old forum have been archived here: https://sites.google.com/a/broadinstitute.org/legacy-gatk-forum-discussions/ You can search for it there and find those resources.

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  Nicolas Rochette

  • May 27, 2022 17:09
  • Edited

  old answer https://sites.google.com/a/broadinstitute.org/legacy-gatk-forum-discussions/2017-01-18-2016-08-11/8323-Why-do-MQRankSum-and-ReadPosRankSum-not-appear-in-some-vcf-file-entries

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  Nicolas Rochette

  • May 27, 2022 17:41
  • Edited

  arguably it's a bug that this is even a warning ("warning: input is normal" pattern)

  other than confusing the users and producing huge log files this leads to things like the silencing of warnings with `--verbosity ERROR` in the Broad's own primates-germline pipeline

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  Andy Lee

  • January 14, 2025 00:23

  The links no longer work, is there a up-to-date archive? 

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  Gökalp Çelik

  • January 16, 2025 13:25

  I am not sure what happened to our legacy archive but this issue is simple.

  Short answer: You cannot have rank tests without alternate alleles so those annotations can only be calculated for sites that are heterozygous. 

  Wayback machine seems to have captured this page successfully. 

  https://web.archive.org/web/20210408180627/https://sites.google.com/a/broadinstitute.org/legacy-gatk-forum-discussions/2017-01-18-2016-08-11/8323-Why-do-MQRankSum-and-ReadPosRankSum-not-appear-in-some-vcf-file-entries 

  Regards. 

   

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