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Capture uploaded allele correctly for VCF input #1744

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Capture uploaded allele correctly for VCF input #1744

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likhitha-surapaneni
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@likhitha-surapaneni likhitha-surapaneni commented Aug 20, 2024 •
edited by nakib103
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Ticket: ENSVAR-5858

  • Fix Unit tests
  • Review header and output columns

@likhitha-surapaneni likhitha-surapaneni marked this pull request as draft August 20, 2024 10:50
@likhitha-surapaneni likhitha-surapaneni marked this pull request as ready for review August 21, 2024 09:20
@nakib103 nakib103 self-requested a review August 21, 2024 09:27
nakib103
nakib103 requested changes Aug 22, 2024
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@nuno-agostinho nuno-agostinho removed their request for review September 6, 2024 12:47
@likhitha-surapaneni likhitha-surapaneni changed the base branch from postreleasefix/113 to main December 4, 2024 15:30
nakib103
nakib103 requested changes Dec 9, 2024
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modules/Bio/EnsEMBL/VEP/Parser.pm
Comment on lines +970 to +971
# Updating a flag to minimise multi-allelic variants in split_variants/rejoin_variants
$vf->{minimised} = 1;
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Multi-allelic is not getting minimised for default format. For example - 1 961320 961324 GCAGG/GCA/GCAG +

But in the output still getting MINIMISED=1, (without the PR they are also not minimised but there is no MINIMISED=1).

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Hi @nakib103 , can you please test this example with the latest commit. The allele is expected to be similar to when running --minimal

@likhitha-surapaneni likhitha-surapaneni changed the base branch from main to postreleasefix/114 December 17, 2024 13:44
@dglemos dglemos requested review from dglemos and nuno-agostinho and removed request for nuno-agostinho January 30, 2025 09:57
@dglemos dglemos self-assigned this Jan 30, 2025
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dglemos commented Jan 31, 2025

The MINIMISED is missing from the header, so in the VCF output even when the variant is minimised this info is not in the file. The only outputs with this info are the default and json.

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dglemos commented Jan 31, 2025

When the input is in VCF format, example:
1 961320 . G GCAGGCTCGGCC . . .

In the vep default output, the Uploaded_variation is represented with minimised alleles:
1_961321_-/CAGGCTCGGCC
In this scenario matching the alleles is more difficult.

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