multiallelic splitting of with ALT asterisk

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#594 2 comments 0 reactions 0 assignees View on GitHub

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Assessment

Difficulty
5/5
Estimated time
Over a week
Newbie friendliness
25/100
Issue type
Feature
Clarity
Needs clarification
Activity status
Stale
Tech stack
c
Domain
bioinformatics

Research direction

Start with the bcftools norm -m- entry point and review how multiallelic records with a * ALT are represented and split. Resolve the expected handling of deleted alleles, then document or implement the decision and validate it with representative records; the issue does not name a source file or test.

Written by the indexing model from the issue text.

Description

What's the expected behavior when applying norm -m- to split multiple alleles when there is a * ALT?

After filtering against gnomad to get rare variants I'm left with a large number of high AF variants with * ALTs.

My understanding is that an asterisk is used to represent a deleted allele when combined with another variant. An asterisk could represent multiple underlying deletions at different positions. After splitting I'm tempted to just delete them.

Dominant language
C
Stars
891
Forks
277
Avg merge
2d 23h
Merged PRs (30d)
2

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