How to get Haplotype file from PLINK format data
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5.4 years ago
bha ▴ 80

My original data is in PLINK format (.bim, .bed , .fam). can I get haplotype file from this plink data? The format of haplotypes should be, with one row per SNP and one column per haplotype.

What program can do this? Any suggestion please

SNP PLINK • 2.6k views
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Where do you next want to use the data? - HaploView? Plink has a --recodeHV option for that. In addition, one cannot just output haplotypes 'randomly' from genetic data. You have to define certain thresholds for parameters that are commonly used to identify haplotypes.

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I just found that SHAPEIT, can do the same.

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