Input Formats

Haplogrep supports input data in a text-based (*.hsd), VCF or fasta format.


For alignment, bwa version 0.7.17 is used. For each input sequence, HaploGrep excludes positions from the tested range that are (1) not covered by the input fragment or (2) has marked with a N in the sequence.

hsd Format

You can also specify your profiles in the original HaploGrep hsd format, which is a simple tab-delimited file format consisting of 4 columns (ID, Range, Haplogroup and Polymorphisms).


You can upload a compressed multi-sample VCF file (vf.gz).

Sample1 1-16569 H100 263G 315.1C 750G   1041G   1438G   4769G   8860G   9410G   12358G  13656C  15326G  16189C  16192T  16519C
Sample2 1-16569 ? 73G   263G    315.1C 750G 1438G   3010A   3107C   4769G   5111T   8860G   10257T  12358G  15326G  16145A  16222T  16519C

For readability, the polymorphisms are also tab-delimited (so columns >= 4). A hsd example can be found here.