Allele Dosage for VCF export

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Mar 11, 2021, 12:14:43 AM3/11/21

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Hi Chris,

I just wanted to clarify this as I've had a read around but couldn't find a straight answer.

The documentation for --export A states that :

'By default, REF alleles are now counted (this is a change from PLINK 1.x)'

Is this true if I export using --export VCF-4.2 vcf-dosage=DS-force as well? I'm importing a .bgen file.

Thanks in advance!

Letitia

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Mar 11, 2021, 1:02:45 AM3/11/21

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No, read the header line for FORMAT/DS: it has one entry per ALT allele.

"--export A" only has one entry per variant; thus, since plink2 supports multiallelic variants, REF allele dosages was the only reasonable default.

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Mar 11, 2021, 6:20:18 PM3/11/21

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Thanks Chris! Much appreciated for the clarification.

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