HaploGrep2 Update 2.1.0

We just updated HaploGrep2, with the following minor points:

  • the Export of the Extended Report (Export / Haplogroup Extendet (txt)) got extended with the “Found_Polys” – see Describtion below:
  • The Report for the potential Phantom Mutations got corrected, so that positions with bases according the rCRS reference are not listed anymore.
  • Report of the possible Recombinations based now on Hamming Distance instead of Kulczynksi-Distance.
  • 6 haplogoups were labeled wrong with H2 instead of H:
previously until 2.0.3
correct in 2.1.0
H2+195 H+195
H2+195+146 H+195+146
H2+152 H+152
H2+16129 H+16129
H2+16291 H+16291
H2+13708 H+13708

Currently, the following columns are included:

SampleID – the identifier of the sample

Range – Sequenced / Genotyped positions on the mitochondrial genome

Haplogroup – resulting Haplogroup

Cluster – if first hit is ambiguous, the result of the cluster is listed in this column

Overall_Rank – the haplogrouping score (from 0.5 to 1) where 0.5 is indicates no SNPs found, and 1 is a perfect match. Now always with “.” as decimal separator

Not_found_Polysfalse negatives – mutations expected in this haplogroup but not found

Found_Polystrue positives – mutations found for the resulting haplogroup. Backmutations are considered as well, indicated by ! (see 182T! or 195C! in Sample Africa01)

Remaining_Polys – Variants not being used for this haplogrouping classification – indicates: a) possibly new haplogroup, or b) possible sample admixture, or phantom mutation (false positives). Listed here are hotspot mutations as well as local private mutations (found in at least one different haplogroup) or global private mutation (unknown in the current phylogeny), as well as heteroplasmic mutations or reference identical positions (the latter is often the case for MicroArray based data).

AAC_Remaining – the remaining Variants in the previous column are checked – and marked as such if involved in an Amino Acid Change.

Input_Sample – the profile used for the classification


HaploGrep 2 Stand-alone Version

With some delay, we finally updated the stand-alone Version of HaploGrep to the latest version 2. This includes the latest Phylotree 17 (Forensic Science International: Genetics Supplement Series, from December 2015), finescaling the human phylogeny even further. This version has no file-upload limit asĀ  currently applied on the web service (file size of 5MB and max. 3,000 samples – you can use compressed files in zip format tough). We also provide a command-line version of haplogrep2, which makes it straight-forward to integrate it in your workflows or pipelines directly. Or you can use the Rest-API for doing so.

Here’s the direct link to the Download Page – enjoy – and don’t hesitate to contact us in case of questions, suggestions, or any kind of problems.

And here’s the evolution of HaploGrep’s sessions per month from Google analytics, with the release of the Phylotree Versions: