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mskcc / vcf2maf

Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms
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Remove --af_esp flag as it's deprecated #324

Closed bozbezbozzel closed 5 months ago

bozbezbozzel commented 2 years ago

This flag stops vcf2maf from running with vep 107 (haven't tested it for earlier versions)

ckandoth commented 2 years ago

Thanks for this. Unfortunately, vcf2maf's output became the standard MAF format that includes two columns for these ESP allele frequencies. So, we'll leave the columns in, but it will never have data in the rows.

The only think pending is to remove the ESP data from the test dataset, so that the Travis CI tests can pass. I'd appreciate if you can add this to the PR. If not, the earliest I can get to it is January.