mthap: an mtdna haplogroup analysis tool

Any discussions regarding mt-DNA markers, results or questions.

Posts: 49
Joined: Sat Mar 17, 2012 5:38 am
PostPosted: Tue Nov 06, 2012 2:44 am
stoeni wrote:I have 263G, 8860A and 15326A


That would be H2a2 then.

Posts: 49
Joined: Sat Mar 17, 2012 5:38 am
PostPosted: Tue Nov 13, 2012 4:40 am
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Posts: 49
Joined: Sat Mar 17, 2012 5:38 am
PostPosted: Sat Nov 24, 2012 11:56 pm
New beta now has initial Geno2.0 support: http://dna.jameslick.com/mthap-new/
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Posts: 286
Joined: Mon Apr 23, 2012 6:15 pm
PostPosted: Sun Nov 25, 2012 7:51 pm
jlick wrote:New beta now has initial Geno2.0 support: http://dna.jameslick.com/mthap-new/

That sounds fantastic James! Great work as always!
DNA/Admixture Central Europe (Alps, Tyrol, Dolomites, Raetia); Y-DNA J2a-L1064, J2a-L210, R1a-M17, R1b-U106 (L48-); mtDNA J1b1b, J1c1d, U5a2b2, U5b1b1. Projects : J2-M172, J2a-PF5197, Alpine DNA, ISOGG Wiki

Posts: 49
Joined: Sat Mar 17, 2012 5:38 am
PostPosted: Thu Dec 13, 2012 7:41 am
Thanks to the latest batch of Geno 2.0 results being released and tremendous community support, I'm now up to 18 samples received of Geno 2.0 mtDNA raw data files. mthap is also on the 13th beta release with Geno 2.0 support with steady improvement being made as each new sample is analyzed.

The main issues being resolved with new samples have been:

  • Confirming orientation of probes with no-calls across all samples. This is now down to 52 markers.
  • Identifying probes which give frequent miscalls.
  • Handling of probes returning heterozygous calls.

The good news is that I'm now reaching the point of diminishing returns on the above points where most new samples exhibit few or no new issues to resolve.

There are two situations in particular that I'd like to focus on, so if you have or know someone who has one of the following, it would be especially important to contribute a Geno 2.0 raw data sample:

  • 8281-8289 deletion. There is a SNP for this deletion but I have no idea how it reports the presence of the deletion. If you have this deletion as confirmed by sequencing or are in a haplogroup which has this deletion, please let me know.
  • Heteroplasmy. There are indications that heteroplasmy may be detectable in some situations. Most heterozygous calls I've seen are suspected or confirmed miscalls, but there is one unconfirmed example that looks like heteroplasmy. If you have confirmed heteroplasmy, please let me know.

Also for everyone who has submitted samples, if you also have sequencing (full sequence OR HVR) or 23andMe data available and have not already provided it, please send those to me for comparison. Most of the blacklisted probes can be determined just by comparing with the other redundant probes and other samples, but it is always better to have another source to compare with. I will be doing another complete review of all the blacklisted probes before final release.
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Posts: 286
Joined: Mon Apr 23, 2012 6:15 pm
PostPosted: Thu Dec 13, 2012 6:29 pm
Great work again James! Looking forward to get the first Geno 2.0 raw data file.
DNA/Admixture Central Europe (Alps, Tyrol, Dolomites, Raetia); Y-DNA J2a-L1064, J2a-L210, R1a-M17, R1b-U106 (L48-); mtDNA J1b1b, J1c1d, U5a2b2, U5b1b1. Projects : J2-M172, J2a-PF5197, Alpine DNA, ISOGG Wiki

Posts: 49
Joined: Sat Mar 17, 2012 5:38 am
PostPosted: Wed Dec 19, 2012 8:43 am
FYI, Genographic 2.0 raw data files being released this week appears to be in a new format that is difficult to interpret accurately. mthap is unable to use this new format at this time.
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Posts: 286
Joined: Mon Apr 23, 2012 6:15 pm
PostPosted: Thu Dec 20, 2012 5:47 pm
I have heard some SNPs are omitted, but not that the format changed also. No worries, probably the Beta phase is over when I get the raw data.
DNA/Admixture Central Europe (Alps, Tyrol, Dolomites, Raetia); Y-DNA J2a-L1064, J2a-L210, R1a-M17, R1b-U106 (L48-); mtDNA J1b1b, J1c1d, U5a2b2, U5b1b1. Projects : J2-M172, J2a-PF5197, Alpine DNA, ISOGG Wiki
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Posts: 542
Joined: Mon Oct 22, 2012 8:19 am
Location: Family Line Veneto ( italy ) since ~1600
YDNA:
T1a2-Z19945
MtDNA:
H95a
PostPosted: Mon Dec 24, 2012 7:29 pm
why is it that when I run the advanced program and use RSRS option I get results only for

Markers found (shown as differences to rCRS):

?

Has the program not been updated for RSRS
Fathers mtdna - T2b17 ...back to 1860 Bucciol line
Grandfathers mtdna - T1a1e ...back to 1820 Mestriner line
Sons Mtdna - K1a4 ....back to 1840 Tesser line
Maternal grandfather ydna - Ild-P109

Posts: 49
Joined: Sat Mar 17, 2012 5:38 am
PostPosted: Tue Dec 25, 2012 12:16 am
No, the RSRS support is not completed yet. If you use the beta version you will sometimes see some options which are incomplete or not working correctly.
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