(some) indels do not follow vcf standard

macarthur-lab / gnomad_browser

gnomAD browser pre-ASHG 2018

MIT License

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(some) indels do not follow vcf standard #44

Closed my-umd closed 3 years ago

my-umd commented 7 years ago

E.g., for the exom set: 1 324677 rs764720704 ACCTCACCAGGCCCAGCTCATGCTTCTTTGCAG A,TCCTCACCAGGCCCAGCTCATGCTTCTTTGCAG

vcf standard requires repeating of the common leading base. But the example (2nd variant) doesn't.

janrehker commented 6 years ago

Good catch! If I get the docs for the vcf standard right, the second one should actually be a separate variant on 1 324676

nawatts commented 3 years ago

This repository is no longer maintained. If this is still an issue in VCFs for the current gnomAD release, please file an issue on broadinstitute/gnomad_methods.