HaploGrep specifications

Information


Unique identifier OMICS_07994
Alternative name HaploGrep2
Interface Web user interface, Application programming interface
Restrictions to use None
Input format VCF
Output data An overview of the classification results.
Programming languages Java
Computer skills Basic
Version 2.0
Stability Stable
Maintained Yes

Taxon


  • Animals
    • Homo sapiens

Maintainer


  • person_outline Hansi Weissensteiner <>

Additional information


http://haplogrep.uibk.ac.at/faq.html

Information


Unique identifier OMICS_07994
Alternative name HaploGrep2
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input format VCF
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Advanced
Version 2.1.1
Stability Stable
Maintained Yes

Taxon


  • Animals
    • Homo sapiens

Versioning


Add your version

Maintainer


  • person_outline Hansi Weissensteiner <>

Additional information


http://haplogrep.uibk.ac.at/faq.html

HaploGrep articles

HaploGrep citations

 (3)
2018
PMCID: 5784966

[…] accurately identify haplogroups than genotyped-only snps (from the illumina humaexome array), we performed the following analysis: i) we determined which haplogroups were present in our data using haplogrep2; ii) we then extracted the full profile for each of these from phylotree17; iii) from these profiles we selected only snps present on the illumina humanexome array to create […]

2017
PMCID: 5780123

[…] the electropherograms from sanger sequencing or igv data. penetration score was calculated as a number of hl individuals among all matrilineal relatives in a family. haplogroups were determined with haplogrep 2 (v2.1.0) and mitomaster tools (37,38)., real time pcr screening for the m.7511t>c mutation was performed on the viia7 system (life technologies, carlsbad, ca, usa) using an assay […]

2014
PMCID: 4045902

[…] sequence were realigned to rcrs (revised cambridge reference sequence [115] using all the quality control steps that we used for calling variants. the variants were used to call haplogroups using haplogrep software [116]. the data conversion from vcf file to haplogrep input file (.hsd file) was performed manually., hypervariable segment (hvs1) sequence of 553 natives saudi arabia […]

HaploGrep institution(s)
Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, Innsbruck, Austria; Department of Database and Information Systems, Institute of Computer Science, University of Innsbruck, Innsbruck;, Austria; Department of Mathematics, University of Hamburg, Hamburg, Germany; Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, and Instituto de Ciencias Forenses, Grupo de Medicina Xenómica (GMX), Facultade de Medicina, Universidade de Santiago de Compostela, Calle San Francisco s/n, Galicia, Spain
HaploGrep funding source(s)
The project was supported by the Austrian Cancer Society/Tirol and by the Tyrolean Science Fund (Tiroler Wissenschaftsfonds).

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