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Converting 23andMe raw data

asked 2019-04-20 09:03:55 -0700

Frederick Karayan gravatar image

updated 2019-04-25 10:48:26 -0700

Greetings, I am attempting to convert my raw 23andMe v4 raw data using the steps outlined by Jeffrey Moore on his YouTube channel. In the conversion wizard preview, the genotypes field is missing. Unfortunately I am unable to post a screen shot because this is my first post to this community. In the Preview box, I see all fields except genotypes.

To clarify, the input fields I see are: Ref/Alt, Identifier, Reference, Alternates, 0/1 Genotypes, Samples. The missing field is Genotypes. I don't know if this normal since the video was posted in 2015 and the version has since changed, or if this is due to a problem parsing the file. Thank you.

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answered 2019-04-25 13:30:23 -0700

Hi there Frederick,

The "0/1 Genotypes" and Samples is the new names of the fields.

I just tried the latest GenomeBrowse and my own 23andMe data. The convert wizard showed no progress during the convert, but CPU was busy and it did complete. One thing to keep in mind is it does require that you have downloaded through the Data Source Library a copy of dbSNP and the the Reference Genome as we use those to get from the RSID fields in the input file to usable genotypes.

We also are not confidendent in the representation of insertions/deletions that 23andMe encodes, and other import tools ignore those, so best to ignore those.

Good luck! Gabe

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Thanks very much for the reply! In my Local Data folder is dbSNP 144, NCBI build CRCh_37_g1k; in User Annotations are Reference Sequence CRCH37 g1k, 1000Genomes build CRCh_37_g1k and RefSeq Genes 105 Interim v1, NCBI build GRCh_37_g1k. Should I externally convert to VCF first then import the VCF?

Frederick Karayan ( 2019-04-25 14:32:08 -0700 )edit
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Asked: 2019-04-20 09:03:55 -0700

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Last updated: Apr 25