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solgenomics / sgn

The code behind the Sol Genomics Network, Cassavabase and other Breedbase websites
https://solgenomics.net
MIT License
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Haplotype matrix download #3853

Open isaak opened 2 years ago

isaak commented 2 years ago

-- could be useful for the mate selection pipelines, among others. (Request from Marnin)

lukasmueller commented 2 years ago

Is this the hapmap file format?

wolfemd commented 2 years ago

Something akin to a dosage matrix but representing haplotypes. Here is what I've done, extracting haplotypes from a VCF: https://wolfemd.github.io/IITA_2021GS/04-PreprocessDataFiles.html#Haplotype_matrix_from_phased_VCF

Uses bcftools convert --hapsample

You can also see the input format I'm aiming for here: https://wolfemd.github.io/genomicMateSelectR/articles/start_here.html#haplotype-matrix-1