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

Question

[Patrick]

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.

Answer 1

[GenoMax]

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

[Patrick]

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?

[GenoMax]

Yes it looks like you will have to do that.