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Fix issue with multi-allelic snps in reference panel #8

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merged 1 commit into from
Sep 27, 2024

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@seppinho seppinho commented Sep 27, 2024

This pull request addresses issue genepi/imputationserver2#28 improving the handling of normalized multiallelic SNPs in the VCF input. The update ensures that all alternate alleles of a multiallelic variant are checked against the reference panel for matches, rather than only the first allele. In case no direct match is possible, the last allele is used for checking strand flips / allelelic swaps. This enhances accuracy when matching variants to the reference panel.

@seppinho seppinho merged commit 513637f into main Sep 27, 2024
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@seppinho seppinho deleted the fixes/quality-control branch September 27, 2024 10:03
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2 participants