Convert 23andme raw data to VCF

When I tried this the script went into an infinite loop with the error message

Use of uninitialized value $dataline in split at 23andme2vcf.pl line 165, <GEN1> line 960613.
Use of uninitialized value $chr in string eq at 23andme2vcf.pl line 166, <GEN1> line 960613.
Use of uninitialized value $pos in numeric gt (>) at 23andme2vcf.pl line 170, <GEN1> line 960613.
Use of uninitialized value $dataline in scalar chomp at 23andme2vcf.pl line 164, <GEN1> line 960613.
Use of uninitialized value $data_line in split at 23andme2vcf.pl line 165, <GEN1> line 960613.
Use of uninitialized value $chr in string eq at 23andme2vcf.pl line 166, <GEN1> line 960613.
Use of uninitialized value $pos in numeric gt (>) at 23andme2vcf.pl line 170, <GEN1> line 960613.

This happened with either my data set or the dataset that was supplied in the folder.

Rich

Same for me. Prints endless "uninitialized values" and took more than a week, until I ended up killing the script.

I have recently pushed a fix for the missing reference position issues. I have also added a means for improving the reference included with the project. When you run your data, if any sites in your data are not included in the reference, the chromosome and position will be noted in a file named "sitesnotin_reference.txt". There is no personally identifying information in this, just genomic positions. If you'd like me to update the included reference to add the reference bases for these sites, just get that list to me, and I will update the included reference.