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.
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
Many of our HaploGrep users are interested in analysing data within automated pipelines. To support users with a scalable and standardized service, we are happy to present you our newest project, called mtDNA-Server.
mtDNA-Server provides a free service for the complete workflow of NGS mtDNA projects. It includes the alignment of FASTQ SE/PE data based on BWA MEM (using JBWA) , sorting of data, creation of BAM files, heteroplasmy detection, contamination identification, haplogroup assignment using of course HaploGrep and graphical report creation based on R.
All steps are parallelized using Hadoop MapReduce. Therefore, we are able to analyse 800 1000G Phase 1 samples (27 GB) on our 30 core test cluster within 30 minutes. To simplify the execution of MapReduce jobs and provide users an intelligent workflow system, we use our MapReduce framework Cloudgene. Cloudgene controls the complete workflow and provides an intelligent queuing system in the background. mtDNA-Server will be available as a download in near future.
For now, we are still in beta and would very much appreciate any kind of feedback!!
Here’s the link:
With the establishment of NGS-Devices and the resulting data flood, new file formats such as FASTQ, SAM, BAM or VCF became de-facto standards in the bioinformatics data world.
Especially the VCF-file containing the variants became of special interest in the user requests lately. There are some python scripts available, that convert a VCF file to a HaploGrep hsd file, as well as a publication with a tool that dedicates itself to this topic. To simplify your life, we decided to implement the VCF file import directly into HaploGrep2. You can give it a try with the 1000 Genome mtDNA VCF file from Phase 1:
1000G Phase 1 VCF File
It’s not always straight forward when working with the human mitochondrial DNA, even if it comes to the question: “what reference sequence do you use?” There should be just one reference and the questions therefore obsolete – what however is not the case.
Since the first sequencing of the human mitochondrial genome by Anderson et al. in 1981 the length was defined to be 16,569 base pairs naming it Cambridge Reference Sequence. Even if some years later errors in this first sequencing were corrected by Andrews et al. in 1999, (Genbank NC_012920.1) the new revised Cambridge Reference Sequence (rCRS) was kept the same length – although a deletion on 3107 was found, it was kept by introducing an N. So the 3107N is basically a deletion, kept so that the positions on CRS and rCRS are still comparable.
From many aspects, the choice of an european Haplogroup (H2a2a1) being the reference sequence is not the best one. Therefore Behar et al. proclaimed a new reference sequence in 2012 – a hypotetical one – the so called Reconstructed Sapiens Reference Sequence preserving the historical genome annotation numbering, but not starting with an leaf-sequence in the phylogenetic tree as is the case with the rCRS, but with a “mitochondrial Eve” as root. The two base insertion on 523-524 are represented as NN instead of AC, therefore the RSRS has 3 N positions (523N, 524N, 3107N). Mannis, the father of Phylotree made this table showing the differences between rCRS and RSRS.
We didn’t however change to the RSRS, since we agree with Bandelt et al., that an additional reference sequence causes confusion. But there’s yet another mtDNA reference sequence around, you should be aware of – present in GRCh37/ UCSC Hg19 or the older GRCh36/UCSC Hg18