Haplotype phasing and imputation in Beagle 5.1
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3.4 years ago
kas • 0

Dear members,

Anybody elaborate on the steps for haplotype phasing and imputation in Beagle v5.1. I have plink format files (.ped and .map) and I tried the older version of Beagle (v3.3). It gives .phased as output. But I need .hap output files to use this as input for rehh package. Beagle v5.1 needs plink map file with cM units. But my map file is having only base pair positions. How to convert bp to cM units. Please help me to proceed further.

haplotype-phasing imputation Beagle rehh • 2.6k views
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Do not add answers unless you're answering the top level question. Use Add Comment or Add Reply instead as appropriate. I've moved your post to a comment this time; please be more careful in the future.

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Thank you for correcting my mistake.

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cM is about a million bp. You can just divide your position by 1e6 to get the cM.

Edit: assuming your organism is human.

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