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brentp / slivar

genetic variant expressions, annotation, and filtering for great good.
MIT License
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Issue using adjusted impactful txt #97

Closed team-tomato-salad closed 3 years ago

team-tomato-salad commented 3 years ago

Hi,

I tried to use INFO.impactful with an adjusted list of variants on VEP/CSQ annotations . And I got an error:

[slivar] warning! no IMPACTFUL_CUTOFF specified. INFO.impactful will not be useful

I made sure that I exported the correct path to the adjustes-order.txt. And here is an example of the CSQ header line from my vcf.

INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence annotations from Ensembl VEP. Format: Allele|Consequence|IMPACT|SYMBOL|Gene|Feature_type|Feature|BIOTYPE|EXON|INTRON|HGVSc|HGVSp|cDNA_position|CDS_position

I am wondering why the Slivar isn't reading my txt and if there's a way to work around that.

Thank you!

brentp commented 3 years ago

Hi, thanks for reporting. There was a bug where it was actually not possible to use your own ordering with SLIVAR_IMPACTFUL_ORDER environment variable. I have just fixed that. You can use the default ordering by using unset SLIVAR_IMPACTFUL_ORDER before running slivar. The fix so you can customize will be out later this week and you can also use this static binary. slivar.gz