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Extend Alt contigs option to allow mapping to two haplotypes genomes. #169

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ghuls opened this issue Dec 12, 2023 · 0 comments
Open

Extend Alt contigs option to allow mapping to two haplotypes genomes. #169

ghuls opened this issue Dec 12, 2023 · 0 comments

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@ghuls
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ghuls commented Dec 12, 2023

It would be great if the Alt contigs approach could be extended so SNAP could use two haplotype FASTA files with all chromosomes/contigs and assign better mapping qualities to reads that map to "multiple" places with the same score, but only once in each hapoltype.
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