Dante Labs (WGS)

[MacUalraig]

Any advise on sources for their interpretation?

They contain the reads before they were aligned to the reference genome and made into the BAM (with a tool like bwa). So they are of use in their own right if you want to do a different alignment - did they already give you an hg38 aligned BAM? If so then less use.

[ybmpark]

Their system was under maintenance for about 10 days and it is restored now but my record is entirely wiped out. Even my order history.
They exhibit every characteristic of a fraudulent operation and they are pretty smart; I took the thanksgiving promotion and it is way beyond 2 months so I cannot work out with paypal for refund.
All their replies seem automatically generated.

[MacUalraig]

Their system was under maintenance for about 10 days and it is restored now but my record is entirely wiped out. Even my order history.
They exhibit every characteristic of a fraudulent operation and they are pretty smart; I took the thanksgiving promotion and it is way beyond 2 months so I cannot work out with paypal for refund.
All their replies seem automatically generated.

I've had my results thanks so nice try but a long way short of being fraudulent. Slow - yes. That's why its cheap.

In the DNA business delays are commonplace. For example one of their rivals failed my sample after having had it for five months. Now I'm waiting for sample 2 to be tried.

[ybmpark]

...so nice try ...

nice try at unproked aggression.

[Miqui Rumba]

If you request BAM and FASTQ files both, then theorically you can realign FASTQ with hg38 in usegalaxy.org for example. Problem is I detected some duplicated fastq files and forgotten reverse pairs in some WGZ big data. My WES fastq forward don't pass fastqc and I have terrible problems to align with whole genome (hg37 or hg38 neither, only Bowtie2 and hisat2 in hg38 work). Picard tools has a tool to revert BAM to fastq files although is a risky process.

[MacUalraig]

If you request BAM and FASTQ files both, then theorically you can realign FASTQ with hg38 in usegalaxy.org for example. Problem is I detected some duplicated fastq files and forgotten reverse pairs in some WGZ big data. My WES fastq forward don't pass fastqc and I have terrible problems to align with whole genome (hg37 or hg38 neither, only Bowtie2 and hisat2 in hg38 work). Picard tools has a tool to revert BAM to fastq files although is a risky process.

I'm also having a look at aligning, not sure which direction to go at the moment as I have more hg19 files than hg38 so might try aligning my YSEQ data back to hg19 whilst I await my hg38 Dante BAM/FASTQ.

Has anyone tried running a Dante VCF through ReMap? I had to change this line:
##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">

to
Number=.

ie
##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
which then run but not got it into shape enough to load in IGV yet.

[Jan_Noack]

deleted duplicate post

[Jan_Noack]

I ordered 4th Mar 19, I had a look at the tracking this morning. It came from the US to Sydney, Aust in a couple of days, sat at the airport for a couple of days and was released to go less than 20 miles in the suburbs of Sydney (to me) on 12th Mar.. I just went out to the post box and there it was (Mon 18th). I logged on again and its been deleted from the USPS tracking system but I have an email from Dante saying its arrived. If I just looked at the USPS tracking no, it would lead me to think the package had not yet arrived at their site "tracking Number: LZ009036991US
Status
Label Created, not yet in the system" and yet an hour ago it gave me the full tracking history.
When in Australia, after the airport there is no tracking just standard ost, and yet they seem to know it has been delivered.
Unfortunately the free return post box only works in the US.... so that will be $3 without tracking or $24 with tracking for return post. Seems a tad wasteful to give me a free return USPS box for use in the US only?

Anyway so far not anything fraudulent at all..as well as others receiving results, I'm hopeful.

I haven't done any computing for about 35 years now..so I'm not up to scratch with the latest tech, LOL.. but I'm hoping someone may be able to tell me when I get these results back what to do.. or maybe just send them to Full Genomes for processing?

I'd love to be able to merge the FTDNA bigY results and YSTR 111 results to the file produced from Dante though.. in theory, it seems it should be easy enough. Has anyone done this? ie merge BAM's. or some other format or would this only be possible with the raw data?. Guess I need to know the formats and spend a load of time getting "into" it all. Just seems that should be the way to go to get the best of both worlds with the processing (if at all possible), in the WGS 30X AND the deeper testing of the smaller no of FTDNA SNPs and STRs.


Anyone doing this or would Full Genomes take all your testing and merge them? I feel a bit more comfortable with Full genomes than YFull as some said that Y Full was in Russia? I haven't check this though. ..and not biased much , but maybe the US seems "safer" long term with data .. probably much of a muchness though. I gather most esend to YFull but I think Full Genomes does the same for about the same cost?

[MacUalraig]

YFull and FGC are both run by fine people who are well respected in the community. I use YFull for analysis and yes I use their payment system too (as I cannot stand PayPal nor they me). Probably best if we leave it at that rather than start up on which foreign countries do this or that with your data!

[Tonev]

YFull and FGC are both run by fine people who are well respected in the community. I use YFull for analysis and yes I use their payment system too (as I cannot stand PayPal nor they me). Probably best if we leave it at that rather than start up on which foreign countries do this or that with your data!

I found a discussion here from 2015 (https://anthrogenica.com/showthread....8-YFull-vs-FGC). Are there more recent comments on the topic?