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scholl-lab / vcf-filtering

A collection of scripts for filtering annotated variant call format files
MIT License
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Bug: Edge case 0/2 in GT field and G,A in Alt fields #39

Closed berntpopp closed 1 month ago

berntpopp commented 1 month ago

Description:

There is an edge case in the GT field when it contains "0/2" and the ALT field has multiple alleles such as "G,A". The script should issue a warning and handle this gracefully.

Example:


9       140128982       T       G,A in Alt fields     NA      2293.64 4,1     407     SLC34A3 NM_001177316.2  missense_variant&splice_region_variant  MODERATE        c.1208T>A       p.Met403Lys     D,D,D,D B,B,B,B D,D,D,D 23.2,23.5       95,2    6       1       Uncertain_significance  5380-N1-DNA1-WES1(0/1);5551-N1-DNA1-WES1(0/2);5636-N1-DNA1-WES1(0/1);5277-N1-DNA1-WES1(0/1);5652-N1-DNA1-WES1(0/1)   891     5       4