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Dante

From SNPedia


There have previously (March 2018) been quality issues with their genotyping data https://www.reddit.com/r/promethease/comments/7vq82s/promethease_report/ These have apparently been resolved. More recently there are issues with the VCF file of their sequencing data. They have been unresponsive to inquiries from User:Cariaso

The VCF problem is illustrated in this example:

Here is the first non-header line from a file:

chrM    1       .       G       <NON_REF>       .       .       .       GT:DP:GQ:MIN_DP:PL      ./.:5:15:5:0,15,155

the important part is

./.

in fact, every single line in the file you've provided contains that.

according to the spec https://samtools.github.io/hts-specs/VCFv4.2.pdf


GT : genotype, encoded as allele values separated by either of / or |. The allele values are 0 for the reference allele (what is in the REF field), 1 for the first allele listed in ALT, 2 for the second allele list in ALT and so on. For diploid calls examples could be 0/1, 1 | 0, or 1/2, etc. For haploid calls, e.g. on Y, male nonpseudoautosomal X, or mitochondrion, only one allele value should be given; a triploid call might look like 0/0/1. If a call cannot be made for a sample at a given locus, ‘.’ should be specified for each missing allele 5 in the GT field (for example ‘./.’ for a diploid genotype and ‘.’ for haploid genotype).

So your file is 100% "missing alleles".

Due to lower volume than the major providers, and general non-responsiveness when the SNPedia admins have emailed them, we're not yet confident of the status or stability of their pipeline and it's compatibility with Promethease. We welcome updates to this page as other users are able to provide updated info.