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brentp / slivar

genetic variant expressions, annotation, and filtering for great good.
MIT License
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unknown attribute:AB error for octopus joint-called VCF #117

Closed mvelinder closed 2 years ago

mvelinder commented 2 years ago

Getting this AB error when using a population called octopus VCF https://luntergroup.github.io/octopus/docs/guides/models/population for two samples I'm using the default slivar-functions.js

$ bash ../slivar_dominant_hht_grch38.sh FamilyR-octopus.vcf.gz.norm.vcf.gz FamilyR.ped 
+ vcf=FamilyR-octopus.vcf.gz.norm.vcf.gz
+ ped=FamilyR.ped
+ fasta=/scratch/ucgd/lustre/work/u0691312/reference/ucgd_reference/GRCh38/human_g1k_v38_decoy_phix.fasta
+ gnomad=/scratch/ucgd/lustre-work/marth/u0691312/reference/gnomad_3.1/gnomad.genomes.v3.1.sites.slivar.zip
+ js=/uufs/chpc.utah.edu/common/HIPAA/u0691312/bin/slivar/js/slivar-functions.js
+ slivar_static expr --vcf FamilyR-octopus.vcf.gz.norm.vcf.gz --ped FamilyR.ped --pass-only --js /uufs/chpc.utah.edu/common/HIPAA/u0691312/bin/slivar/js/slivar-functions.js -g /scratch/ucgd/lustre-work/marth/u0691312/reference/gnomad_3.1/gnomad.genomes.v3.1.sites.slivar.zip --info 'INFO.gnomad_popmax_af < 0.01 && INFO.gnomad_n_hets < 50 && INFO.gnomad_n_homalt < 10' --family-expr 'dominant:fam.every(segregating_dominant)' -o FamilyR-octopus.vcf.gz.norm.vcf.gz.slivar.vcf.gz
> slivar version: 0.2.2 186b862063ce50ee1d282bc610196630c4ecac61
[slivar] 2 samples matched in VCF and PED to be evaluated
[slivar] message for /scratch/ucgd/lustre-work/marth/u0691312/reference/gnomad_3.1/gnomad.genomes.v3.1.sites.slivar.zip:
   > created on:2020-12-12
[slivar] javascript error. this can some times happen when a field is missing.
error from duktape: unknown attribute:AB for expression:fam.every(segregating_dominant)

[slivar] occured with variant:chr1  50481   .   G   GGTGTGT 62.55   PASS    AC=1;AN=4;DP=58;MQ=41;NS=2;gnomad_popmax_af=0.000122699;gnomad_popmax_af_filter;gnomad_n_hets=2;gnomad_n_hets_filter;gnomad_n_homalt=0;gnomad_n_homalt_filter   GT:GQ:DP:MQ:PS:PQ:FT    0|0:32:39:47:50299:100:PASS 0|1:9:19:22:50299:7:PASS
[slivar] continuing execution.
[slivar] javascript error. this can some times happen when a field is missing.
error from duktape: unknown attribute:AB for expression:fam.every(segregating_dominant)

[slivar] occured with variant:chr1  54712   .   T   TTTTTTTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTC  32.34   PASS    AC=1;AN=4;DP=134;MQ=55;NS=2;gnomad_popmax_af=0.000143761;gnomad_n_hets=3;gnomad_n_homalt=0  GT:GQ:DP:MQ:PS:PQ:FT    0|1:28:34:48:54676:100:PASS 0|0:378:100:57:54676:100:PASS
[slivar] continuing execution.
[slivar] javascript error. this can some times happen when a field is missing.
error from duktape: unknown attribute:AB for expression:fam.every(segregating_dominant)

[slivar] occured with variant:chr1  54712   .   T   TTTTTTTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTC  32.34   PASS    AC=1;AN=4;DP=134;MQ=55;NS=2;gnomad_popmax_af=-1;gnomad_popmax_af_filter;gnomad_n_hets=0;gnomad_n_hets_filter;gnomad_n_homalt=0;gnomad_n_homalt_filter   GT:GQ:DP:MQ:PS:PQ:FT    1|0:28:34:48:54676:100:PASS 0|0:378:100:57:54676:100:PASS
[slivar] continuing execution.
[slivar] javascript error. this can some times happen when a field is missing.
error from duktape: unknown attribute:AB for expression:fam.every(segregating_dominant)

[slivar] occured with variant:chr1  54724   .   C   CTT 307.3   PASS    AC=1;AN=4;DP=137;MQ=54;NS=2;gnomad_popmax_af=-1;gnomad_n_hets=-1;gnomad_n_homalt=-1 GT:GQ:DP:MQ:PS:PQ:FT    0|1:307:43:50:54676:100:PASS    0|0:378:94:56:54676:100:PASS
[slivar] continuing execution.
[slivar] javascript error. this can some times happen when a field is missing.
error from duktape: unknown attribute:AB for expression:fam.every(segregating_dominant)

[slivar] occured with variant:chr1  54730   .   TTC T   33.83   PASS    AC=1;AN=4;DP=139;MQ=54;NS=2;gnomad_popmax_af=-1;gnomad_n_hets=-1;gnomad_n_homalt=-1 GT:GQ:DP:MQ:PS:PQ:FT    1|0:33:48:50:54676:100:PASS 0|0:408:91:56:54676:100:PASS
[slivar] continuing execution.
[slivar] javascript error. this can some times happen when a field is missing.
error from duktape: unknown attribute:AB for expression:fam.every(segregating_dominant)

[slivar] occured with variant:chr1  83903   .   AAGAAAGAAAG A   256.94  PASS    AC=2;AN=4;DP=66;MQ=52;NS=2;gnomad_popmax_af=-1;gnomad_n_hets=-1;gnomad_n_homalt=-1  GT:GQ:DP:MQ:PS:PQ:FT    1|1:21:20:43:83903:58:PASS  0|0:121:46:55:83903:100:PASS
[slivar] continuing execution.
[slivar] javascript error. this can some times happen when a field is missing.
error from duktape: unknown attribute:AB for expression:fam.every(segregating_dominant)

[slivar] occured with variant:chr1  83972   .   GAA G   32.38   PASS    AC=2;AN=4;DP=72;MQ=51;NS=2;gnomad_popmax_af=0.00066353;gnomad_n_hets=25;gnomad_n_homalt=0   GT:GQ:DP:MQ:PS:PQ:FT    1|1:21:21:40:83903:58:PASS  0|0:121:51:55:83903:100:PASS
[slivar] continuing execution.
[slivar] javascript error. this can some times happen when a field is missing.
error from duktape: unknown attribute:AB for expression:fam.every(segregating_dominant)

[slivar] occured with variant:chr1  83974   .   AAAAG   *   11.23   PASS    AC=2;AN=4;DP=74;MQ=51;NS=2;gnomad_popmax_af=-1;gnomad_n_hets=-1;gnomad_n_homalt=-1  GT:GQ:DP:MQ:PS:PQ:FT    1|1:28:21:40:83903:58:PASS  0|0:11:53:55:83903:100:PASS
[slivar] continuing execution.
[slivar] javascript error. this can some times happen when a field is missing.
error from duktape: unknown attribute:AB for expression:fam.every(segregating_dominant)

[slivar] occured with variant:chr1  99083   .   C   TTTTTTTTT   102.33  PASS    AC=2;AN=4;DP=270;MQ=45;NS=2;gnomad_popmax_af=-1;gnomad_n_hets=-1;gnomad_n_homalt=-1 GT:GQ:DP:MQ:PS:PQ:FT    0|1:23:109:47:99072:20:PASS 0|1:79:161:43:99072:24:PASS
[slivar] continuing execution.
[slivar] not reporting further errors.

Any ideas? I tried to lower the min_GQ and min_AB in the 

var config = {min_GQ: 20, min_AB: 0.22}

line. But no luck.

Any ideas? I can give you a test VCF if that'd help. Thanks Brent!

brentp commented 2 years ago

Hi Matt, you're using the default js for rare disease which tries to access AB. (or AD if that doesn't exist). You'll have to run octopus with the --annotations (I think) argument to tell it to output AD. Or you can modify the slivar-functions.js to remove AB stuff.

mvelinder commented 2 years ago

--annotations AD worked like a charm. Thanks again dude!