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View Full Version : Full Genomes Corporation sale and a new Big Y BAM file analysis service



DebbieK
04-26-2014, 12:07 AM
News of a sale at Full Genomes Corporation and a new Big Y BAM file analysis service.

http://cruwys.blogspot.co.uk/2014/04/a-new-bam-file-analysis-service-from.html

Kwheaton
04-26-2014, 02:50 AM
Thanks Debbie! Good news on an otherwise Terrible, No Good, Very Bad DNA Day from the standpoint of the new Haplogoop!

TigerMW
07-10-2014, 03:49 PM
Amazingly enough, I've actually got my own .bam file in my hands now.

I just saw where Chris Morely also has some kind of analysis service he is calling ClarifyDNA.

What are the benefits that FGC offers in terms of analysis versus Clarify DNA or YFull?

News of a sale at Full Genomes Corporation and a new Big Y BAM file analysis service.

http://cruwys.blogspot.co.uk/2014/04/a-new-bam-file-analysis-service-from.html

Muircheartaigh
07-10-2014, 06:16 PM
Amazingly enough, I've actually got my own .bam file in my hands now.

I just saw where Chris Morely also has some kind of analysis service he is calling ClarifyDNA.

What are the benefits that FGC offers in terms of analysis versus Clarify DNA or YFull?

Mike,

Recent posts suggest that Clarify DNA analyses Big Y VCF and Bed files so it's not working with the original raw material. Yfull and FGC both analyse the BAM file.

I've had my FCC results analysed by Yfull. They provided a list of my shared SNPs and a separate list of Novel Variants which more or less agreed with the FGC analysis. The results are not in a form that you can manipulate and there is no comparison files like the ones provided by FGC.

I submitted my Big Y results to FGC for their analysis. The format of the results they provide is superb and leaves FTDNA report in the dark. Your results will be compared to others in their database which is updated with each new set of results and includes 1K Genomes, PGP, FGC and presumably Big Y results that have already been submitted to them. Your known SNPs will be labelled and any new ones they discover will be given an ID. The file is more or less chronological, with the highest volume of shared Variants at the top and lowest number at the bottom. They also provided a separate file in EXCEL comparing my results with approximately 40 of my closest matches, from DF13* downwards. It included 2 anonymous PGP candidates from the PGP project who are clearly part of our 253-1716-11 cluster.

As the files are in EXCEL you can manipulate the results and I used my FGC file as a template for Analysing the Big Y results of the 253-1716-11 cluster currently numbering seven. I would definitely recommend anyone with Big Y results to take advantage of the FGC offer.

I also recommend that you use a BAM file analysis tool to examine one by one the Variants included in your Big Y results. You are likely to find that a number of them are unreliable. I use the IGV software which provides a pictorial view of the read sequences in the vicinity of the variant location, so you can see what are obviously misaligned reads and dodgy variants.

Ray

VinceT
07-10-2014, 08:05 PM
I encourage folks to send their BAM files to both Full Genomes Corp and YFull.com, as those services use slightly different filtering and qualitative assessment algorithms. The SNPs identified by both services should have the highest quality potential, and those should then be forwarded to YSEQ.net and FTDNA for further SNP primer development. Either service may identify candidate SNPs that the other had filtered out, which may prove useful for matching against future samples.

Full Genomes registers their "FGC" SNPs with http://ybrowse.isogg.org, and YFull flags their SNPs on their experimental tree at http://yfull.com/tree/ if shared by two or more samples.