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How to convert a 23andme.txt file to a vcf file?

Hi,

I am trying to convert a file from 23andme to a vcf file. The file is tab delimited txt file.

I tried using

bcftools convert --tsv2vcf input.tab.gz -f ref.fa -s SampleName -Ob -o sample.bcf

but I am not sure how to get ref.fa where can I download it? I looked here but I don't know which file to download and whether I need to unzip it or do anything else with it before I can use it.

is there a detailed tutorial somewhere, that explains exactly what to to convert 23andme to vcf?

I am pretty new to this topic so any help is appreciated.

23andme vcf
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updated by GenoMax GenoMax • written by Patrick • Patrick

1 answer

You will need to know which reference genome build your file used. There are two recent (relative) genome builds GRCh37 and GRCh38.

GRCh38 reference can be downloaded from (large file): http://ftp.ensembl.org/pub/current_fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz

GRCh37 reference can be downloaded from: http://ftp.ensembl.org/pub/grch37/current/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.dna.primary_assembly.fa.gz

Here is a prior thread that may be helpful: bcf convert 23andme to vcf

• 0 views • link
written by GenoMax GenoMax

Thanks for your reply. Do I need to unzip the file after downloading it or do anything else with it? It's a .fa.gz but in the command it says .fa?

• 0 views • link
written by Patrick • Patrick

Yes it looks like you will have to do that.

• 0 views • link
written by GenoMax GenoMax

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