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Old 11-01-2018, 12:48 PM   #1
juni711
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Location: North Carolina

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Default Comparing whole genome sequence to commercially available DNA test kits

Greetings,

I apologize in advance if I have posted in the wrong thread, or am posting that has been covered before. I am new to this forum. Some background info: I have become interested in genealogy as of late, and have found gedmatch.com to be very resourceful. Utilizing one of the commercially available DNA test kits, I was able to determine that my ancestry includes Native American, likely Native Caribbean (Taino) as my parents both are from Puerto Rico. None of the commercially available DNA testing companies can distinguish North American vs South American ancestry, they simply lump everyone into two overlapping groups. One of the many problems with commercially available DNA test kits is that participants are not able to distinguish how they are related, especially so when Native American ancestry is involved.

Gedmatch.com is a website that allows the public to upload their raw DNA to produce test kits to allow the direct comparison between individuals that is not available on commercial DNA testing companies. Some Genomes from previous research (i.e. Clovis-Anzick-1) have been uploaded to gedmatch.com, which allows members to compare and see if they share common ancestry with these individuals (http://www.y-str.org/p/ancient-dna.html).

I have found a research article that sequenced a Lucayan Taino from the Bahamas (of a female that was around 500 years before the arrival of Columbus) and is available on

Original Research article on Lucayan Taino:
http://www.pnas.org/content/115/10/2341

Sequenced genome deposited in European Nucleotide Archive:
https://www.ebi.ac.uk/ena/data/view/PRJEB22578

The individual that previously uploaded ancient sequenced genomes to Gedmatch has stopped doing so (he has gone on to other endeavors). I would like to upload the Taino genome unto Gedmatch, but whole genomes can not be added on. There is a way to change from a FASTQ file to a BAM file, and eventually run a program "BAM Analysis Kit" which in turn would convert the BAM file into a VCF file which can be used to upload to Gedmatch. I have been able to download the FASTQ file, and converted it to a BAM File, but the BAM analysis kit tends to crash and the times I were able to run it, it would only spit out analysis for the first three chromosomes.

Just hoping that someone here can assist me in either trying to run the program or finding another way to modify the BAM file (of the above sequenced genome) into a format that is comparable to formats used by commercial DNA testing. Any information anyone can provide will be greatly appreciated.

Last edited by juni711; 11-01-2018 at 12:50 PM.
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Old 11-01-2018, 05:21 PM   #2
cmbetts
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It looks like the BAM Analysis Kit software is trying to do a whole lot more than generating a VCF file (replicating commercial genealogy reports). If what you need is a VCF file, there are many tools to do that directly (google Variant Caller) with lots of opinions on which one is the best.
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