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evotools / hapbin

Efficient program for calculating Extended Haplotype Homozygosity (EHH) and Integrated Haplotype Score (iHS)
GNU General Public License v3.0
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Finding a recombination map #68

Open aramesh97 opened 1 year ago

aramesh97 commented 1 year ago

Hello, I am having a lot of trouble finding the right recombination map. How do I generate the second column ( Locus ID) since most maps only give me genetic and physical position?

Also what should I do if the loci detected in my map file and vcf file is differently numbered?

Third and last question is can I use a VCF file which has been generated straight out of imputation for the purpose of this tool input?

aramesh97 commented 1 year ago

I would greatly appreciate your help on this James, I am working on a critical project @prenderj

prenderj commented 1 year ago

Hi

Locus ID is just an ID for the variant. This can be whatever you want. For example an rs ID or just string indicating location.

Your hap and map files need to have the same set of variants in them. If they dont then will need to filter to the intersect.

Yes can use genotypes from a phased VCF but will need to convert it to the required format as described in the FAQ section

aramesh97 commented 1 year ago

Thank you, just to reiterate the locus I’d can literally be serial numbers then? Like locus1..2..3..4 as stated in you example file

prenderj commented 1 year ago

Yes

On Tue, 20 Sept 2022, 17:13 aramesh97, @.***> wrote:

Thank you, just to reiterate the locus I’d can literally be serial numbers then? Like locus1..2..3..4 as stated in you example file

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