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Clinical-Genomics / genmod

Annotate models of genetic inheritance patterns in variant files (vcf files)
http://moonso.github.io/genmod/
MIT License
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No "GeneticModels=" in the output #88

Closed jielab closed 6 years ago

jielab commented 6 years ago

Hi, there,

Please see my test.vcf and test.ped file pasted at the bottom. Please use *sed 's/ /\t/g'** in case the TAB are pasted into multiple spaces.

After I run genmod models test.vcf --family_file test.ped, there is no GeneticModels= written to the output for some reason. Can you please kindly let me know what I missed or did incorrectly?

Thank you & best regards, Jie

========== test.ped =========

FamilyID SampleID Father Mother Sex Phenotype

CEU ON180102131 0 0 1 1 CEU ON180102132 0 0 2 1 CEU ON180102133 ON180102131 ON180102132 1 2

=========== test.vcf ========

fileformat=VCFv4.1

INFO=

INFO=

INFO=

contig=

reference=file:///humgen/gsa-hpprojects/GATK/bundle/current/b37/human_g1k_v37.fasta

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT ON180102131 ON180102133 ON180102132

1 12908 . C A 67.13 PASS AC=1;AF=0.167;AN=6;BaseQRankSum=3.638;ClippingRankSum=0;DP=96;ExcessHet=3.0103;FS=0;MLEAC=1;MLEAF=0.167;MQ=26.68;MQRankSum=0.04;QD=2.24;ReadPosRankSum=-0.647;SOR=0.075;Annotation=DDX11L1,WASH7P GT:AD:DP:GQ:PL 0/0:33,0:33:99:0,99,995 0/0:33,0:33:67:0,67,955 0/1:24,6:30:98:98,0,651 1 13302 . C T 202.99 PASS AC=1;AF=0.167;AN=6;BaseQRankSum=4.727;ClippingRankSum=0;DP=116;ExcessHet=3.6798;FS=4.754;MLEAC=2;MLEAF=0.333;MQ=36.12;MQRankSum=-5.329;QD=4.61;ReadPosRankSum=-3.402;SOR=1.514;Annotation=DDX11L1,WASH7P GT:AD:DP:GQ:PL 0/1:31,13:44:99:229,0,589 0/0:42,0:42:2:0,2,855 0/0:30,0:30:0:0,0,587

jielab commented 6 years ago

Hi, I think now I found the reason for the error:

  1. I must put samples in the order of father-mother-proband in the VCF file;
  2. I could not have the "PL" field in the VCF file.

Once I fixed the above two issues. Now it works fine. Please try this out and fix this bug.

Thank you!

Best regards, Jie

moonso commented 6 years ago

Hi Jie,

the reason why no models are annotated are that no models are followed in your example. The proband(affected child) has is ON180102133 according to the ped file. In your vcf it is the second column of the individuals. It has genotype 0/0 for both variants so no models are followed in this case.