Question: How to use minimac3 to impute genotypes from a SNPmatrix dataset
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gravatar for caesar_etos
6 days ago by
caesar_etos0 wrote:

I am trying to use minimac3 to impute genotypes of a dataset given as SNPmatrix (I guess). I understand that minimac3 takes VCF files as input, so my main question is:

  • Is there a way to convert a SNPmatrix to VCF?

As I am not sure whether the dataset is given in SNPmatrix, below is the first 2 rows of the dataset given:

Chr startPos endPos SNPID S1 S2 S3 S4 S5 S6 S7 S8 S9 S10 S11 ...

1 15812664 15812665 rs2861484_G_T 0 1 0 0 1 1 0 0 0 1 2 ...

where Chr denotes chromosome and S denotes sample.

Other related questions are:

  • Is this file format called SNPmatrix? or what is it known as in the genetics community?
  • By looking at this dataset, how to tell if it is phased/unphased? note that genotypes info are encoded only by 0, 1 and 2 only
  • Are there other imputation tools that can take SNPmatrix as input?
ADD COMMENTlink modified 6 days ago • written 6 days ago by caesar_etos0
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