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I have a vcf file that contains SNPs from chromosome 2 for 2000 samples. I want to create a genotype matrix from this vcf file.

The file is in zipped format as well so that I can use bcftools. I want to filter snips with

  • MAF>= 1%
  • more than 2 alleles.

I'm not quite sure why I have to filter for more than 2 alleles, is it common to do this if I'm trying to perform PCA analysis?

The instruction I'm using right now is:

bcftools query -e'AF<0.01' -e'AF>0.99' chr2.vcf.gz | \
  sed 's/0|0/0/g' | sed 's/0|1/1/g' | sed 's/1|0/1/g' | sed 's/1|1/2/g' | \
  grep -v "|" > extract.tab
  • How do I only extract the multi-allelic cases?

I have a way to do it using bcftools view -m2 chr2.vcf.gz but the results seem fishy.

  • How do I correct this?
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  • $\begingroup$ What do you mean 'the results seem fishy'? Can you post a small sample input and output. $\endgroup$
    – user438383
    Apr 5, 2020 at 7:33

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