HaploGrep Help

User Manual


HaploGrep2 Screencast

Data sensitivity

Since data is transfered to our server located in Innsbruck, a wide array of security measures are in force:
  • - The complete interaction with the server is secured with HTTPS.
  • - Input data is deleted from our servers as soon it is not needed anymore.
  • - The single accesses are secured via a cookie session management and all data is deleted after the session runs out.
  • - A logging tool controls of inappropriate software behavior and monitors the status of HaploGrep.

HaploGrep Usage Statistics

Since the update of HaploGrep 2 in August 2015, the web server was accessed by 3,000 users from 80 countries. Since its publication in Human Mutation in 2010, over 20,000 users accessed HaploGrep. To find out who used HaploGrep see Google Scholar

HaploGrep File Formats

HaploGrep supports the previously introduced HSD file format and since the new version Haplogrep2 also VCF.
HSD details: the first column contains the sample ID, the second column specifies the targeted genetic region (any sequenced range and any genotyped SNP, also in any combination), the third column can include the assumed haplogroup status (or left blank if not specified), and then the polymorphisms are indicated separated by tab stops. The first line of each file includes the column descriptions ("headers") for SampleID, Range, Haplogroup and Polymorphisms and is therefore not imported into HaploGrep. An example can be found as textfile or as .zip. Open the file with any spreadsheet application (MS Excel) and edit it! Alternatively , this format is generated automatically with our freely available epidemiological data management system eCOMPAGT (published in BMC Bioinformatics). The direct Import of fasta files is in available in beta version.

Phylogenetic data basis

We are using the data of Phylotree, a phylogenetic tree of global human mitochondrial DNA variation and process it in an automatic fashion.