Parameters
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 > |