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Dante Labs

From SNPedia

A least expensive option, but with numerous user reports of problems.

Their BAM file is accessible at a url like https://s3-eu-west-1.amazonaws.com/datareleasedante2/F12FREEABCD1234-04_HUMabcR_123456767_12344545/result/1234567890346_WGZ/result_alignment/1234567890_WGZ.bam and can be given to promethease via 'Import from URL'. The URL is visible on their page via "Inspect Element". Inspect tutorial.

There have previously (March 2018) been quality issues with their genotyping data https://www.reddit.com/r/promethease/comments/7vq82s/promethease_report/ were eventually resolved.

As of April 2019 they are planning to have their own lab in Italy and use Oxford Nanopore PromethION https://twitter.com/olivierlucas29/status/1113395481839919104 for long read sequencing.

VCF Issues[edit]

An earlier 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.

BAM Issues[edit]

In May of 2019 we're diagnosing BAM issues at https://www.reddit.com/r/promethease/comments/btbjvt/weird_dante_labs_results_situation_plz_help/

Their 30x WGS BAM files should be around 100GB; Promethease will process it just fine without the accompanying index file (.bam.bai). For sanity checking, the BAM file should be about equal in size to the rest of the files on the drive combined, +/- a few GB.