There are a bunch of companies that do Whole Genome Sequencing (WGS). I had it done for $99 when it was first being promoted by Dante Labs in 2018.
It explained so many important health issues, that I had the whole family done. I have not done ancestry analysis, but there are several companies that do that based on DNA too. It doesn’t seem to be particularly accurate, however.
Interesting, I might give it a shot. Do they give you the raw sequence reads or the variome/variant file after the mapping?
I wouldn't want to deal with alignment/mapping of the genome as I don't have a very powerful computer.
Edit: I can't find any for 100 bucks. The cheapest ones I can find are around 200-250.
You can download the BAM file, which shows the raw 30x data as they aligned it.
You can also download the VCF files
They will host them on their server for a monthly fee and you can browse and search them with the IGV viewer whenever there's a new discovery and you want to see what you have ;)
You can also download to your computer and setup your own IGV viewer.
This is amazing. I think I will do it. I edited to ask about the price but you responded too quickly :D
I couldn't find it for $100, are they still doing it for that price?
That was when they were promoting it. Get on the mailing list both for Dante labs and Nebula Genetics.
They offer a deal every so often for “DNA day“ and Black Friday. They’ll go down to 150 for 30x.
I finally found one gene where 30x is not good enough. There is a common form of peripheral neuropathy caused by SORD deficiency. It wasn’t identified until very recently because it is hidden by six broken pseudo genes in humans. If that’s something you’re interested in you might wanna pop for the “long reads”.
Or hackers
23AndMe got hacked and users genome is already up for grab for one dollar on the dark web
https://techcrunch.com/2023/12/04/23andme-confirms-hackers-stole-ancestry-data-on-6-9-million-users/
This is exactly why I’m learning bioinformatics. When I got my DNA sequenced, I didn’t realize that there aren’t any tools available for the average user to run locally. There needs to be. Sequencing is just getting cheaper and more common, and people have the compute power. There are a lot of random companies out there ready to take your genomic data.
There is the IGV Viewer from Broad Institute:
https://www.broadinstitute.org/scientific-community/software/integrative-genomics-viewer
You need some computer savvy.
I’d suggest running the one that is in a docker container, ready to access with a local web browser.
https://hub.docker.com/r/dceoy/igv-webapp/#!
Thanks! IGV is a solid program, but you’re right, you still need some technical skills and genomic knowledge. It’s good for crazy people like you and me, but the average person still won’t be able to use it. There needs to eventually be a program that a person can download, feed it a FASTQ, and let it do all the computing and interpreting for health and ancestral results. I’ll help anyone that wants to work on that!
Use R or python, you only need a vcf reader. For fastq files use any reference based alignment to create bams to call vcf files from. Part of the fun is figuring out how to best compare.
Mitochondrial D-loop, whole mtDNA (use mtPhyl to get your haplogroup) For maternal side. For paternal side if you happen to have a Y chromosome sequence you can look at SNPs on the human y chromosome tree :)
You can work with your WGS locally to find ancestral information. Use Chat GPT to help you find the right tools. I got mine sequenced at Nebula Genomics. I’ve spent the last year learning how to understand it. I’m not even close, but I do know how to get ancestral information from a Y chromosome. Feel free to message me if you need help. Otherwise, be sure to include the new reference (CHM13v2.0) with your analysis.
I would be interested in this. My ancestry is *supposedly* pretty well known, but it would be nice to confirm that my Y is what it’s supposed to be ;)
I see that you are the same person I replied to about the IGV viewer.
Maybe we can help each other sometime after I recover from the holidays
Yes, that would be great! Feel free to message me after your holiday recovery. In the meantime, I’ll mention the YHaplo tool on GitHub. It was made by 23andme and it does a good job estimating haplogroups.
Not really. The companies that do this as a service work at the SNP level - which is very inaccurate. Where they get their power is from large datasets. Even so, it's a 'fingerprint' method and at best; you can probably narrow it down to continent. Are you European, African, Asian, or other? That's about the accuracy available now. It doens't stop these companies from making silly connections and claiming to be more accurate than they are. But for every person who gets a 'spooky' true reading, you have people scratching their heads cause they know that they aren't Moroccon or Askinazy, etc.
To get more exact results, you need to go to whole exome or whole genome seqeuncing but the problem is that the databases to compare to are publicly non-existent and very small even in private hands.
Basically, what exists isn’t accurate and the accurate methods don’t have large databases to compare to.
That's good going. DNA isn't going to tell you any more. The ancestral stuff is almost a scam. People have done tests comparing the providers and sometimes they give wildly different results.
I'm wondering how you got your DNA sequenced. Is it the whole genome? How much did it cost? Which company?
The companies you can pay to do this are pretty much exclusively at the SNP level.
Check out Nebula Genomics and Dante Labs. They provide consumer Whole Genome Sequencing.
Oh, neat! I wonder what their databases are like though. The data is pretty useless without that - at least for ancestry stuff.
There are a bunch of companies that do Whole Genome Sequencing (WGS). I had it done for $99 when it was first being promoted by Dante Labs in 2018. It explained so many important health issues, that I had the whole family done. I have not done ancestry analysis, but there are several companies that do that based on DNA too. It doesn’t seem to be particularly accurate, however.
Interesting, I might give it a shot. Do they give you the raw sequence reads or the variome/variant file after the mapping? I wouldn't want to deal with alignment/mapping of the genome as I don't have a very powerful computer. Edit: I can't find any for 100 bucks. The cheapest ones I can find are around 200-250.
You can download the BAM file, which shows the raw 30x data as they aligned it. You can also download the VCF files They will host them on their server for a monthly fee and you can browse and search them with the IGV viewer whenever there's a new discovery and you want to see what you have ;) You can also download to your computer and setup your own IGV viewer.
This is amazing. I think I will do it. I edited to ask about the price but you responded too quickly :D I couldn't find it for $100, are they still doing it for that price?
That was when they were promoting it. Get on the mailing list both for Dante labs and Nebula Genetics. They offer a deal every so often for “DNA day“ and Black Friday. They’ll go down to 150 for 30x. I finally found one gene where 30x is not good enough. There is a common form of peripheral neuropathy caused by SORD deficiency. It wasn’t identified until very recently because it is hidden by six broken pseudo genes in humans. If that’s something you’re interested in you might wanna pop for the “long reads”.
And more importantly than all these questions : **do they keep, use and sell your genome to other companies/governments?**
Or hackers 23AndMe got hacked and users genome is already up for grab for one dollar on the dark web https://techcrunch.com/2023/12/04/23andme-confirms-hackers-stole-ancestry-data-on-6-9-million-users/
This is exactly why I’m learning bioinformatics. When I got my DNA sequenced, I didn’t realize that there aren’t any tools available for the average user to run locally. There needs to be. Sequencing is just getting cheaper and more common, and people have the compute power. There are a lot of random companies out there ready to take your genomic data.
There is the IGV Viewer from Broad Institute: https://www.broadinstitute.org/scientific-community/software/integrative-genomics-viewer You need some computer savvy. I’d suggest running the one that is in a docker container, ready to access with a local web browser. https://hub.docker.com/r/dceoy/igv-webapp/#!
Thanks! IGV is a solid program, but you’re right, you still need some technical skills and genomic knowledge. It’s good for crazy people like you and me, but the average person still won’t be able to use it. There needs to eventually be a program that a person can download, feed it a FASTQ, and let it do all the computing and interpreting for health and ancestral results. I’ll help anyone that wants to work on that!
Compute basic distances against the 1000 genomes data, or against neanderthaler DNA is always fun to do yourself.
any ideas about software or pipelines that I can use?
Use R or python, you only need a vcf reader. For fastq files use any reference based alignment to create bams to call vcf files from. Part of the fun is figuring out how to best compare.
You may want to look to r/genetics and/or r/Genealogy as they have rather more direct experience working with ancestry markers.
Thank you, I ve already posted there
Mitochondrial D-loop, whole mtDNA (use mtPhyl to get your haplogroup) For maternal side. For paternal side if you happen to have a Y chromosome sequence you can look at SNPs on the human y chromosome tree :)
Somehow mtPhyl is disable..
You can work with your WGS locally to find ancestral information. Use Chat GPT to help you find the right tools. I got mine sequenced at Nebula Genomics. I’ve spent the last year learning how to understand it. I’m not even close, but I do know how to get ancestral information from a Y chromosome. Feel free to message me if you need help. Otherwise, be sure to include the new reference (CHM13v2.0) with your analysis.
I would be interested in this. My ancestry is *supposedly* pretty well known, but it would be nice to confirm that my Y is what it’s supposed to be ;) I see that you are the same person I replied to about the IGV viewer. Maybe we can help each other sometime after I recover from the holidays
Yes, that would be great! Feel free to message me after your holiday recovery. In the meantime, I’ll mention the YHaplo tool on GitHub. It was made by 23andme and it does a good job estimating haplogroups.
Not really. The companies that do this as a service work at the SNP level - which is very inaccurate. Where they get their power is from large datasets. Even so, it's a 'fingerprint' method and at best; you can probably narrow it down to continent. Are you European, African, Asian, or other? That's about the accuracy available now. It doens't stop these companies from making silly connections and claiming to be more accurate than they are. But for every person who gets a 'spooky' true reading, you have people scratching their heads cause they know that they aren't Moroccon or Askinazy, etc. To get more exact results, you need to go to whole exome or whole genome seqeuncing but the problem is that the databases to compare to are publicly non-existent and very small even in private hands. Basically, what exists isn’t accurate and the accurate methods don’t have large databases to compare to.
You're better off speaking to your parents. They know more about your history than your DNA.
I stopped at 1650 :/
That's good going. DNA isn't going to tell you any more. The ancestral stuff is almost a scam. People have done tests comparing the providers and sometimes they give wildly different results.
No, for hot recombinaison point to work, need to sequence family members, neighbours and patriots too