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Haplotype Construction Using Phase Version 2.1

It would be great if someone can help with Haplotype construction using PHASE version 2.1. I have genotyped data in Plink format and not really sure how to convert it to PHASE version 2.1 INPUT format in easy way. Thanks.

haplotype

You can use plink for recoding plink format to fastPHASE by ''--recode-fastphase'' option in PLINK. It’s similar to PHASE input file format, you should just add S for SNP and M for microsatellite marker on 4th raw as locus type

A good idea, but it seems multiallelic sites in vcf would be converted to missing alleles...

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