Converting a BAM/VCF into genetic recombination map tsv file

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3.8 years ago

taniamahmood38 ▴ 60

Hii, I am using Selscan for XPEHH, iHS analysis. For these tests, a genetic recombination map tsv file with four columns: (Chromosome, Position(bp), Rate(cM/Mb), Map(cM)) is required. Currently, i have a BAM file and a VCF file. If anyone please sort out how can i convert either my BAM or my VCF file into the required file format. Please guide.

Thanks in advance!

.tsv file format --GeneMap SelScan BAM/VCF • 1.5k views

ADD COMMENT • link 3.8 years ago by taniamahmood38 ▴ 60

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You should be able to download more or less the right thing from here http://bochet.gcc.biostat.washington.edu/beagle/genetic_maps/

ADD REPLY • link 3.8 years ago by 4galaxy77 2.9k

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Many thanks for helping. This is the perfect file i want but i require GeneMap file of Goat (Capra hircus) instead of human. Is it possible to get that one for goat ? Sorry to trouble but this link contains the GeneMap file for human only.

ADD REPLY • link 3.8 years ago by taniamahmood38 ▴ 60

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Ah right. I will have a look - but if you want to search, I would suggest looking for either 'goat genetic map' or 'goat recombination map'.