Louis Kessler’s Behold Blog The Behold User Forum
Entries, Comments and Posts
251.
Creating a Raw Data File from a WGS BAM file - Blog entry by lkessler - 12 May 2019
I was wondering in my last post if I could create a raw data file that could be uploaded to to GEDmatch or DNA testing company from my Whole Genome Sequencing (WGS) results. I was trying to use one of the Variant Call Format (VCF) files. Those only include where you vary from the human reference. So logically ...
252.
WGS – The Raw VCF file and the gVCF file - Blog entry by lkessler - 7 May 2019
As I noted in my last post, Whole Genome: The VCF File, Part 2, the SNP VCF (Variant Call Format) file that Dante Labs gives tester of WGS (Whole Genome Sequencing), does not quite have everything that is needed to generate a raw data file that can be uploaded to various DNA sites for people matching. ...
254.
My Whole Genome Sequencing. The VCF File - Blog comment by lkessler - 6 May 2019
Bizlovr: These files are not easy to work with. I'm trying to directly analyze them myself (I have some skills with this sort of analysis) since I don't like the black box analysis tools that the genomic genealogists use. Getting down and dirty and playing with the ants is easier for me than just getting ...
255.
Comparing Raw Data from 5 DNA Testing Companies - Blog comment by lkessler - 6 May 2019
Ian: If you’ve already done Ancestry, then I’d recommend 23andMe as the other one which will give you the greatest number of different SNPs to use. Only 13% of Ancestry and 23andMe’s SNPs were in common and you should end up with about 1.1 million SNPs by combining just those two tests. Also you’ll get ...
256.
Combine Kits into One Superkit on GEDmatch Genesis - Blog comment by spmcdonald - 5 May 2019
Could you combine kits from siblings, e.g., uncles, with the same parents to get a “super uncle” kit?
257.
Comparing Raw Data from 5 DNA Testing Companies - Blog comment by ianbd - 4 May 2019
I am wondering if there is a chart or list somewhere showing the actual overlaps, not just the counts? I have already done the Ancestry DNA, but instead of doing all the other ones to make a combined file, Which would be the best two to followup with in order to obtain the greatest total SNP coverage. Right ...
258.
My Whole Genome Sequencing. The VCF File - Blog comment by blzlovr - 2 May 2019
I received my data from Dante Labs and didn't know what to do with it, the medical information was very similar to Genos and Promethease. The kit I bought included mtDNA but couldn't figure out a way to view it so I asked customer service and they added a VCF file. They said I could get the BAM and FastQ ...
259.
WGS Result Files - Blog comment by lkessler - 23 Apr 2019
Kendraz: When I purchased my kit back in August 2018, the hard drive with the BAM and FASTQ files was included free of charge. I did note in November that they started charging $69 extra for the hard drive containing your raw data.
I am purely looking at the short versus long reads for the purpose of ...
260.
Whole Genome: The VCF File, Part 2 - Blog entry by lkessler - 22 Apr 2019
A couple of months ago, I compared my VCF file to my DNA test results. The Variant Call Format (VCF) file is given to you when you do a Whole Genome Sequence (WGS) test. That test finds your DNA values for your whole genome, all 3 billion positions, not just the 700,000 or so positions that a standard DNA ...
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Combine Kits into One Superkit on GEDmatch Genesis - Blog comment by lkessler - 6 May 2019