Exporting haploid and diploid allele dosage from vcf file on chrX

[Mathias Gorski]

Dear all,

I am trying to export the allele dosages oon chrX by this command:

plink2 \
        --pfile "$infileBgen"  \
        --extract $SNP_list_file \
--export vcf vcf-dosage=DS-only \
        --out "$outfilename"

but I get the error
"Error: --export vcf-dosage=DS-only mode can only be used with all-diploid data."

It is clear to me, that males are not coded all-diploid. I am fine with the haploid allele dosage in males and the diploid allele dosage in women. 

Is there a way to get these out in vcf format? I would then afterwards separate the men from the women ... or is it necessary to separate the data one step before into men and women and then to extract via DS-only?

Thank you in advance!

best, Mathias

[Chris Chang]

You can use "--export vcf vcf-dosage=DS" for chrX, since the ploidy information is encoded in the GT field in that case.  Or "--export Av" if you're mainly trying to generate a variant-major text matrix.

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[Mathias Gorski]

Hi, 

this is extremely helpful and solved my problem!

Thank you so much! 

Best, Mathias