how to merge genetic map of ChrX nonPAR with PAR1 and PAR2 for imputation?
I am trying to impute with beagle my vcf calls on chromosome X. The Beagle website provides a plink genetic map file for GRCh38 with ChrX, PAR1, PAR2. I get an error when I try to run my VCF with them. I tried manually merging them but I guess the Cm would be off? How can I merge the 3 files into one ChrX genetic map? If the recombination rates are inaccurate in the PAR regions how is this typically handled?
Thanks
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