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slowkoni / rfmix

RFMIX - Local Ancestry and Admixture Inference Version 2
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Can rfmix be used in other species except for hunman #22

Open liufy11 opened 4 years ago

liufy11 commented 4 years ago

genetics maps is required for rmfix . but my study object is not hunman . so I can't download genetics map from website . Is rmfix only suit for hunman ,or should I make a genetic map special for my object ?

slowkoni commented 4 years ago

Just make up a genetic map if you don’t have one. RFMix will interpolate genetic distance when a marker’s physical (sequence map) location in base-pairs is between anchor points of a genetic-distance-to-physical-distance mapping. So if you were to just assume 1cM/Mb, then just put 0 and the maximum position per each chromosome, and set the genetic position for 0 to 0 cM and 100000000 to 100.0 cM, if 100 Mbp were at least as large as the largest physical coordinate on that chromosome. Or whatever, you should get the idea here...

On Sep 18, 2019, at 06:36, liufy11 notifications@github.com wrote:

genetics maps is required for rmfix . but my study object is not hunman . so I can't download genetics map from website . Is rmfix only suit for hunman ,or should I make a genetic map special for my object ?

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