After you have successfully installed Haplogrep on your local system, you can now run it with the following command.

./haplogrep3 classify

Required Parameters

The following parameters are mandatory.

Parameter Description
--tree Select one of the available trees
--in Please provide the input file name
--out Please provide an output name

Optional Parameters

Besides the mandatory parameters, we also provide numerous parameters for specific use cases.

Parameter Description
--metric, distance To change the classification metric to Hamming Distance (hamming) or Jaccard (jaccard) add this parameter (Default: Kulczynski Measure).
--extend-report For additional information on SNPs (e.g. found or remaining polymorphisms) please add the --extend-report flag (Default: off).
--tree Specify one of the installed trees.
--chip If you are using genotyping arrays, please add the --chip parameter to limit the range to array SNPs only (Default: off, VCF only). To get the same behaviour for hsd files, please add only the variants to the range, which are included on the array or in the range you have sequenced (e.g. control region). Range can be sepearted by a semicolon ;, both ranges and single positions are allowed (e.g. 16024-16569;1-576;8860).
--skip-alignment-rules Add this option to skip our rules that fixes the mtDNA nomenclature for fasta import. Click here for further information. Applying the rules is the default option since v2.4.0
--hits To export the best n hits for each sample add the --hits parameter. By default only the tophit is exported.
--write-fasta Write results in fasta format.
--write-fasta-msa Write multiple sequence alignment.
--hetLevel=<value> Add heteroplasmies with a level > from the VCF file to the profile (default: 0.9).