With HaploGrep version 2.1.21 the handling of human mitochondrial FASTA sequences gets a new improvement. As we use BWA 07.17 for the alignment of FASTA sequences, the mtDNA nomenclature is not always met by default. Therefore we provide a new parameter which will fix the nomenclature to the correct one used in Phylotree, finally yielding a better HaploGrep score. The parameter is:
Currently we apply 66 rules, which will fix issues around indels (insertions and deletions) – e.g. the deletion on 8281-8289d for haplogroup B, but also around 315 and 524 (which are however not relevant for the mitochondrial phylogeny)
What triggers an Error and what is considered a Warning in HaploGrep2? Here’s a short overview of the events:
- The detected haplogroup quality is low. Sample is marked red. Quality <=80%
- The expected haplogroup is not a super group of the detected haplogroup
- Common rCRS polymorphism not found! The sample seems not properly aligned to rCRS.
- The sample seems to be aligned to RSRS. Haplogrep only supports rCRS aligned samples.
- The sample misses >2 expected polymorphisms
- Fasta Alignment check: positions to recheck
- The detected haplogroup does not match the expected haplogroup but represents a valid sub haplogroup
- The sample shows ambigous best results
- The sample contains heteroplasmic positions
- The detected haplogroup quality is moderate. Sample is marked yellow. Quality <= 90% and > 80%.
- The sample contains polymorphimsms that are equal to the reference / The sample contains variants according the rCRS
- The sample contains >2 global private mutation(s) that are not known by Phylotree
- The sample contains >=2 local private mutation(s) associated with other Haplogroups
- Different haplogroup with 2 local private remaining mutation(s) found
- The sample contains undetermined variants N
2 haplogoups were labeled wrong and are fixed now – thanks Rocio for pointing out!
|previously until 2.1.0
|correct in 2.1.1
HaploGrep2 currently accepts only single file uploads. To merge several VCF files to one, several tools exist:
An example based on the VCFtools can be found here:
# For each VCF file:
tabix -p vcf Variants_sample_A.raw.vcf.gz
vcf-merge *.raw.vcf.gz >| Variants_all_samples.raw.vcf
Hope this helps!
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
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_Polys – false negatives – mutations expected in this haplogroup but not found
Found_Polys – true 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
Happy to announce the publication of the HaploGrep2 paper in this years Web Server Issue 2016 in Nucleic Acids Research. For data generated with massive parallel sequencing devices in form of fastq or bam files, the mtDNA-Server paper also published in this years issue, gives some details there.
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 as 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:
Here’s the overview of the new export options, HaploGrep 2 offers, by clicking on the small arrow next to Export:
Missing a specific export format? Feel free to contact us!
After exactly 2 years, Phylotree, the “database” behind HaploGrep got updated by Mannis van Oven. Here’s the accompanying publication on Phylotree 17 . The mtDNA tree has now 5,437 haplogroups, which is a growth of over 13% to the previous version. Find out how Phylotree 17 differs for your dataset, by using the updated HaploGrep 2 Version, with the latest mtDNA tree build 17.
The 1000 Genome Consortium recently released the Phase 3 mitochondrial DNA data of over 2,500 samples for download, besides their papers in Nature, stating:
Mitochondrial chromosome variants are now available for the Phase 3 individuals from our FTP site
Since in the current Version HaploGrep 2 can deal with the VCF file (unzipped), all 2500 samples can be analyzed instantly