23andme2vcf

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hg18 reference

1

hi rob, i tried using your script for converting the 23andme data from the personal genome project. it appears that data is still aligned to hg18. could you proivde the...

tikacp

My file looks like this: ``` rs548049170 1 69869 TT rs13328684 1 74792 -- rs9283150 1 565508 -- ``` But the reference document in the cloned repo looks like this:...

ghost

Broken genotypes

2

I keep getting just "0" or "1" for genotype after ~560,000 correct conversions using the 23andme_v4_hg19_ref.txt.gz data and after ~500,000 correct conversions using the 23andme_v4_hg19_ref.txt.gz data using "perl 23andme2vcf.pl genome_XYZ.vcf...

lhelseth

MT reference incorrect

2

It appears that you have used UCSC's reference hg19 instead of NCBI's GRCh37 to build your own reference. Normally this is fine, but there are differences between these builds at...

tylerwmarrs

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

3

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...

teyden

New reference

5

Hi Rob, thanks for the script, do you mind committing the code that generates the reference file, my says 8140 sites were not included even with version 4. Many thanks.

EugeneBragin

This may take some significant development. The exact coordinates and alleles involved in the insertions and deletions signified by the I's and D's in the genotype column of the 23andme...

arrogantrobot