pzm
Any websites do really good ancestry or match known ancient DNA? I've used the WGSExtract tool mentioned earlier to convert and uploaded that output to a few sites, eg mytruenancestry, but in general shouldn't genealogical matches be better with the whole genome than the partial extracts of eg 23andme? The only app for that I've found has been on sequencing.com and it wasn't very detailed. Appreciate any pointers, thanks!
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anorris8
I've used Promethease for my Genos WES data. It looks like Dante is also compatible (here). It's no longer free, but it's not expensive either. 

Something to think about when using VCF:  https://www.reddit.com/r/SNPedia/comments/8ik77i/genos_has_less_info_in_promethease_than_23_and_me/.  Screen Shot 2020-03-22 at 1.55.36 PM.png 


FYI, here is a list of various tools for genome annotation, including genealogy, but most are based on 23andMe (or other SNP chip) formats: https://isogg.org/wiki/Raw_DNA_data_tools
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Erik Chapman
One option is to use the program at this link  http://www.beholdgenealogy.com/blog/?p=3018 to create a huge high quality SNP stack of all SNPs used in the 5 most common SNP sites, which will have the quality of he WGS BAM file it comes from.  Then there won't be the gaps that you get from VCF.

While in some cases the standard variant will have health consequences, in general one would expect the VCF to include anything that is serious. 

The lack of normal variant information isn't really important in that context.  Also beware that SNP sites don't advertise how many reads they use, if they only use one read, I think that's a 99% accuracy rate- but 1% wrong when there are hundreds of thousands of SNPs associated with various diseases can mean thousands of disturbing false positives 

Getting a whole bunch of false positives from a low read test doesn't mean that you're getting more complete information.  

In addition to the false positives, low read tests have an unacceptably high rate of false negatives.   From the Dante reports there are hundreds of variants that could contribute to reduced function, that give some context for each other.   So a low read test may not only produce a lot more information that is wrong, it may be omitting key information that is important.  
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J Man
Is there a way that we can search for individual SNPs from our results?
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Clare86
@J Man Do you mean in the VCF files or in the Data Explorer in Genome Manager.

In the data explorer you can put in an rsid or chr and position to see a particular snp.

For the VCF files you could upload them to sequencing.com. They have an app called Genome Explorer which you can use to search for particular variants. Bear in mind that if you are homozygous for the reference allele then the variant won't be in the vcf file. 
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J Man

@Clare86

I don't see anything that says ''Data Explorer'' on my results page...Maybe the test that I took does not have that tool/feature?

I have uploaded my data to sequencing.com but I can't find the two SNPs that I am looking for when I search for them on there.

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Clare86
@J Man

I assume you are looking for the two variants (rs28445963 and rs72931809) you referenced in the topic you started (Data Explorer). I had a look at my data in sequencing.com and I can't find them in any of the files, fastq, bam or vcf.

Some regions of the genome are harder to sequence than others, it may be that these two variants fall into that category. 
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J Man
@Claire86

One of the tech guys from DANTE Labs told me that they do test for those two SNPs though and he told me that I can search via DNA Explorer which I can't find on my Genome Manager page. He then told me that he is going to have the tech team look into it. This was weeks ago and he has never gotten back to me.
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Clare86
@J Man

I can search for those positions in the DNA Explorer. It's weird you can't see the DNA Explorer. I would email them again.

One thing I did note when looking at the snps is that on some of the reads then the extra details panel shows that the read base and base quality is undefined. This is probably why sequencing.com isn't showing the snp. 
Screenshot 2020-04-03 at 19.38.20.png    
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J Man
Yeah I don't seem to have that on my personal page for some reason. I purchased my test from DANTE Labs during a sale almost 2 years ago. Maybe that's why?
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Erik Chapman
For some reason DNA Explorer is sometimes available when I log in, sometimes not.  It hasn't really been a priority for me so I haven't tried to figure it out or complain about that.   I'm not really sure what I'm supposed to do with it. 
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J Man
I sent an email to DNATE Labs a few days ago about this. Hopefully I get a reply.
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Randy H
DNA Explorer is just their implementation of Broad Institutes' Integrated Genome Viewer (IGV). You can download that tool to any desktop and run locally. Of course, this requires you have your BAM file on your desktop as well.
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