search

23andMe / yhaplo

Identifying Y-chromosome haplogroups in arbitrarily large samples of sequenced or genotyped men
Other
103 stars 24 forks source link

ERROR. Attempted to access haplogroup before assigned: #12

Closed rozaimirazali closed 5 years ago

rozaimirazali commented 5 years ago

Hello. What does this error mean?

Reading genotype data... QGP_MALE_onlyGT.vcf.gz

ERROR. Attempted to access haplogroup before assigned: 0100066181_S5_L005

This is my command:

callHaplogroups.py --input QGP_MALE_onlyGT.vcf.gz --ancDerCounts --haplogroupPaths --derSNPs --derSNPsDetail --ancSNPs --anc SNPsDetail --hgGenos hg

dpoznik commented 5 years ago

Rozaimi, thanks for writing in again.

Short answer: For normal usage, the --hgGenos option is unnecessary, so I suggest omitting it.

Longer answer: The option can provide a useful view of your genotype data at SNPs associated with a specified branch of the Y-chromosome tree, if that's something you're interested in. There are two reasons it didn't work for you:

  1. You need to specify which haplogroup you want to investigate. For example, if you want to look at the root of the Q haplogroup, you would do something like this: callHaplogroups.py --input data/1000Y.subset.genos.txt --hgGenos Q I've updated the metavariable to be haplogroup rather than hg to make this more explicit.
  2. The option was not working for SNP-major input, but it is fixed in version 1.0.18.