23andMe format to vcf

[Jay An]

Hello,

plink has a new function to to convert 23andMe to VCF format, my question is how to input REF and ALT allele into the plink function.

I used plink1.9, if i use command plink --23file xxxx.txt --recode vcf --out xxx, in the result vcf file, there is a lot of "." in allele columns, because there is no allele information.

thanks

Jay

[Christopher Chang]

You can’t convert 23andMe indels to VCF without a file describing what the indel alleles actually are. “—snps-only just-acgt” can be used to throw them out.

plink 2.0’s —ref-from-fa flag can be used to set the correct REF alleles for SNPs.

[Jay An]

thanks Christopher,

1. plink2.0 seems not recognize option --23file. which version should I use?

2. although the REF can be refer to --ref-from-fa, how about ALT allele? if 23andme file gives two REF alleles, the ALT column in vcf will be a dot "." because there is no information for ALT allele in fasta reference, how can I get rid of "." in vcf file?

[Christopher Chang]

1. Use plink 1.9 to convert the 23andMe file to plink binary format, and plink 2.0 for the rest.

2. There's nothing wrong with missing ALT alleles in single-sample datasets, and there's no unique way to fill them in since some of these SNPs have multiple ALT alleles.

[Jay An]

thanks.

is it possible to add xxx.bim file to get ALT allele? because any SNP with ALT "." will be removed in Eagle tool.

[Christopher Chang]

If you have an Eagle reference panel, just get the ALTs from there.  If you don't, you can't use Eagle on a single-sample dataset.