Question: how to generate genetic maps from VCF snps data
0
gravatar for mab658
3 months ago by
mab65820
mab65820 wrote:

Hi Everyone,

Could someone guide me on how to generate genetic map from snps VCF file in order to use it for imputation. I have filtered my snps VCF file and I need genetic map for the imputation. I got to know that one can use PLINK. I need to know what I need to extract from my data prior to using PLINK. Thanks

sequencing snp • 239 views
ADD COMMENTlink written 3 months ago by mab65820

Which imputation program?

ADD REPLYlink written 3 months ago by Kevin Blighe41k

I am using beagle 5.0 program for imputation.

ADD REPLYlink written 3 months ago by mab65820

It looks like you are just asking question after question about imputation using Beagle. What work have you done so far? Have you performed an extensive search on how to create a genetic map?

ADD REPLYlink written 3 months ago by Kevin Blighe41k
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