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brentp / slivar

genetic variant expressions, annotation, and filtering for great good.
MIT License
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slivar tsv #112

Closed sprakashUTH closed 2 years ago

sprakashUTH commented 2 years ago

I used slivar_expr to filter a vcf and am having issues when I try to reformat using tsv. What am I doing wrong?

  1. ./slivar expr --vcf $vcf --ped $ped --pass-only -g gnomad.hg38.v2.zip -g topmed.hg38.dbsnp.151.zip --info 'INFO.impactful && INFO.gnomad_popmax_af < 0.0001 && variant.FILTER == "PASS" && variant.ALT[0] != "*" && INFO.topmed_af < 0.0001 && INFO.highest_impact_order <= ImpactOrder.disruptive_inframe_deletion' --js slivar-functions.js > $cohort.highest.vcf

  2. ./slivar tsv -s slivar_expr -i gnomad_popmax_af -i gnomad_popmax_af_filter -i gnomad_nhomalt -c ANN -g pli.lookup -g clinvar_gene_desc.txt -p $ped $cohort.highest.vcf > $cohort.highest.tsv

slivar version: 0.2.1 ceb97b26cd39d341dd7aa96ddb42239692df5b50 vcf.nim(157) get Error: unhandled exception: slivar_expr not found in header [KeyError]

brentp commented 2 years ago

Hi, slivar tsv mostly works on output from trios. But, in your tsv command, you show -s slivar_expr in order to use that, you would have to have used --trio 'slivar_expr:kid.het ... in the first command.

sprakashUTH commented 2 years ago

I solved that issue by using the "dominant" flag in the first command. How do I get the amino acid change of the variant to export to the tsv? It is not in the default output when I use -c BSCQ or -c ANN.

brentp commented 2 years ago

hi, you can use --csq-column $column where $column matches the name in the description for ANN or BCSQ