1000G Phase 3 mtDNA data available

nature_1000G_phase3

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

Importing VCF file to HaploGrep 2.0

vcf_panes

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