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Allele Frequency(AF) for male and female samples

Hello,

I am trying to compute AF for male and female samples. I know bcftools is able to do it, but I am not sure how it behaves for next case. If I have two samples:

  • chromX pos 10 Female 0/1
  • chromX pos 10 Male 1/1

As you all know, Male has only one chrom X, but normally the vcf software calling gives 1/1 (sometimes even 0/1), how does bcftools know that has to count 3 AN (2 female + 1 male) instead of 4(2 female + 2 male). Could I introduce any kind of information telling that one sample is female and other male?

Thanks!

bcftools vcf
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updated by finswimmer finswimmer • written by roalva1 roalva1

1 answer

Hello,

you can use a combination of bcftools +fixploidy and +fill-AN-AC

The fixploidy plugin needs at least a file with the sex information. It's just a text file which contain one line per sample with the sample name and the sex, e.g.

Sample_1 M
Sample_2 F

It than needs a file with regions where the ploidy should be fixed. The default looks like this:

#CHROM FROM TO SEX PLOIDY
 X 1 60000 M 1
 X 2699521 154931043 M 1
 Y 1 59373566 M 1
 Y 1 59373566 F 0
 MT 1 16569 M 1
 MT 1 16569 F 1

If this default is fine for you, you don't need to create an extra file.

Run the program like this:

$ bcftools +fixploidy input.vcf -- -s sex.txt -p ploidy.txt|bcftools +fill-AN-AC > output.vcf

fin swimmer

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written by finswimmer finswimmer

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