Chromosome column in genetic map does not match the VCFs

sdtemple / isweep

Statistical inference of recent positive selection using IBD segments

https://github.com/sdtemple/isweep

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Closed sdtemple closed 3 months ago

sdtemple commented 3 months ago

You should adjust the first column, the chromosome number, in the genetic map to reflect the VCF #CHROM column. To see what the #CHROM is:

bcftools query -f "%CHROM\n" [your-vcf-file] | head

You should change the genetic map, not the vcf! The VCF may be larger and take longer to edit.