Haplotype Construction Using Phase Version 2.1
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8.6 years ago
MS ▴ 30

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 • 4.3k views
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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

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

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