Aligning 23andme to reference genome

Question

[Manuel]

I've got some 23andMe data that I'm playing around with and was wondering if the SNPs could be aligned to a reference genome to subsequently be turned into a VCF. The txt file has the genomic positions so I guess it's possible? I just don't know which tool and/or parameters should be appropiate.

Here's an example of what the data looks like.

rsid    chromosome  position    genotype
rs548049170 1   69869   TT
rs9283150   1   565508  AA
rs116587930 1   727841  GG

Thanks for any guidance

[Ankit]

Have you tried this?

https://samtools.github.io/bcftools/howtos/convert.html

[Manuel]

Yes I tried something similar. The thing is that when I do it that way, the resulting VCF won't tell me the ALT allele when the result is Homozygous. It looks somethong like this:

CHROM   POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  FAM001_ID001
1   69869   rs548049170 T   .   .   .   PR  GT  0/0
1   565508  rs9283150   A   .   .   .   PR  GT  0/0
1   727841  rs116587930 G   .   .   .   PR  GT  0/0

I wanted to do the alignment so that the resulting VCF shows what the ALT allele is for that rsid.

[Ankit]

In case you want to capture ALT allele, then you can use dbSNP to get ALT allele. If you have rsIDs you can match with SNP database (may be you can use ANNOVAR stored dbSNP or other database)and get coordinates - REF - ALT.

I am not sure about 23andme data if it contains all rsid SNPs or rare unreported variants too.

If alignment is aim then you can request the company for raw data and analyse by yourself.

Hope it helps

[Manuel]

Thanks I'll try that!