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arrogantrobot / 23andme2vcf

convert your 23andme raw file to VCF | DEPRECATED, please see https://github.com/plantimals/2vcf
MIT License
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23andMe SNPs have been updated #2

Closed sjackman closed 11 years ago

sjackman commented 12 years ago

The 23andMe SNPs have been updated, so when I run the script I see this error message:

raw data file and reference file are out of sync at ./23andme2vcf.pl line 153, <GEN1> line 587611.
arrogantrobot commented 12 years ago

I just pushed an update to the reference to match the new probe-set used by 23andme.

sjackman commented 12 years ago

Thanks for the quick response, Rob.

Cheers, Shaun

On 2012-10-17, at 18:47, Rob notifications@github.com wrote:

I just pushed an update to the reference to match the new probe-set used by 23andme.

— Reply to this email directly or view it on GitHub.

neilfws commented 11 years ago

Same error has re-occurred:

raw data file and reference file are out of sync at ./23andme2vcf.pl line 154, <GEN1> line 4.

My 23andme report (V3) contains 991786 SNPs, the reference file contains 960613.

arrogantrobot commented 11 years ago

Thanks for the update! It looks like my raw data still has 960613 records. You can create an updated reference if you have the refseq fasta and samtools with https://github.com/arrogantrobot/hg19_23andme_refs

Just pipe the output of getPos.pl to a file: perl getPos.pl my_raw_data.zip refseq.fa | gzip -c > my_new_23andme_ref.txt.gz

If someone is willing to generate the new reference and issue a pull request, I'd be happy to merge it, or I will push the new reference once my personal 23andme data is updated.

In the mean time, I will see about handling the mismatch more gracefully.