Question

Linkage analysis with whole -exome sequencing data

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8.8 years ago

wanabi ▴ 60

Which software do you recommend to perform classic linkage on whole exome sequencing data?

Thanks

linkage whole-exome-sequencing • 2.6k views

ADD COMMENT • link updated 2.4 years ago by Ram 44k • written 8.8 years ago by wanabi ▴ 60

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I am getting this everytime I am trying to run my PLINK data. Can anyone help me with this problem?

ERROR: No file [ mydata.ped ] exists.

ADD REPLY • link updated 6.2 years ago by Ram 44k • written 6.3 years ago by nudrylab • 0

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ERROR: Problem with compound genotype [ A ] should be two characters long

ADD REPLY • link updated 6.2 years ago by Ram 44k • written 6.3 years ago by nudrylab • 0

Ram · Answer 1 · 2016-02-17

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8.8 years ago

andrew.j.skelton73 6.6k

ADD COMMENT • link updated 6.2 years ago by Ram 44k • written 8.8 years ago by andrew.j.skelton73 6.6k

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Thanks for your reply. However, I dont think you can do classical two-point or multi-point linkage analysis with PLINK or PLINK1.9

Thanks

ADD REPLY • link updated 6.2 years ago by Ram 44k • written 8.8 years ago by wanabi ▴ 60

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Another one I came across recently is SEQLinkage

ADD REPLY • link 6.6 years ago by andrew.j.skelton73 6.6k