Tried to use it, but the output file doesn't contain any rows below the static headers for the .vcf file?

[teyden]

I followed the simple instructions to convert my 23andme downloaded .txt file to a .vcf file, receiving this output response:

gunzip: 23andme_v3_hg19_ref.txt.gz: not in gzip format 587747 sites were not included; these unmatched references can be found in sites_not_in_reference.txt.Try running again, but specify the other reference version: ./23andme2vcf.pl {path to}mysnps.txt mysnps.vcf 4

FYI, I replaced the correct path to the .txt file with {path to} in this issue.

I tried 23andme_v3_hg19_ref.txt.gz version as well, however received the same response, telling me to try the version 4. In either case, the output file (mysnps.vcf) is empty below this section:

`##fileformat=VCFv4.2

fileDate=20151116

source=23andme2vcf.pl https://github.com/arrogantrobot/23andme2vcf

reference=file://23andme_v4_hg19_ref.txt.gz

FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT GENOTYPE

`

Any clue on what's wrong? Please and thanks.

[arrogantrobot]

Teyden,

I have given this a look, and it appears as though 23andme have switched from gzipped tar to zip compression of the exported raw data file. I will address this issue. But it looks like the errors you're seeing are more complex than just a different compression format. I'll dig into this and get back to you ASAP. Thank you for reporting this error!

Rob

[teyden]

Hey, thanks for getting back to me, Rob.

I unzipped the 23andme reference file manually to a .txt file and modified your perl script to handle .txt files and skip gunzipping the previous format. That worked and outputted a vcf file as I would have expected. Analysis didn't work when I uploaded the file to the 1000genomes tool "http://browser.1000genomes.org/Homo_sapiens/UserData/UploadVariations" though. I'm not sure if that's due to the outputted vcf from your perl script or whether it's something wrong with their system. Let me know if you have any thoughts on this at all, or possible sources I can go to to check if my outputted VCF file is of correct format.

Thanks a bunch.

[arrogantrobot]

Not sure what's up with your 1000genomes issue @teyden . Do you still have this issue? Is there an error message associated with it?