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luntergroup / octopus

Bayesian haplotype-based mutation calling
MIT License
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How to annotate the resulting VCF? #98

Closed jlee110 closed 4 years ago

jlee110 commented 4 years ago

Hello,

I keep getting errors from trying to annotate the called variants using Variant Effect Predictor. Is octopus incompatible with VEP? I used "--legacy" and octopus_to_rtg.py to get the somatics only.

Error: Can't call method "isa" on an undefined value at /nfs/public/release/ensweb/latest/live/www/www_98/ensembl/modules/Bio/EnsEMBL/TopLevelAssemblyMapper.pm line 223, <__ANONIO__> line 22970.

Thank you Jay

dancooke commented 4 years ago

Can you provide a sample VCF that's failing?

jlee110 commented 4 years ago

3642_B5_Tum_DNA_legacy.legacy.somatic.vcf.zip

dancooke commented 4 years ago

The record that's failing is

KI270746.1  40540   .   G   GT  103.02  FRF AC=1;AN=3;DP=26;MQ=49;MQ0=0;NS=1;PP=7.41;SOMATIC    GT:GQ:DP:MQ:PS:PQ:MAP_VAF:VAF_CR:FT 0/1:89:26:49:40540:99:0.42:0.27,0.58:FRF

Even if I simplify this to

KI270746.1  40540   .   G   GT  50  .   .

It still fails, which would indicate that this is a problem with VEP, not Octopus.