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.
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