HaploGrep pipeline

HaploGrep specifications

Information


Unique identifier OMICS_07994
Name HaploGrep
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


  • Primates
    • Homo sapiens

Maintainer


  • person_outline Hansi Weissensteiner <>

Additional information


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

Information


Unique identifier OMICS_07994
Name HaploGrep
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


  • Primates
    • Homo sapiens

Versioning


Add your version

Maintainer


  • person_outline Hansi Weissensteiner <>

Additional information


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

Publications for HaploGrep

HaploGrep IN pipelines

 (10)
2018
PMCID: 5827201
PMID: 29483551
DOI: 10.1038/s41598-018-21844-6

[…] in normal tissue, we identified “private” constitutional variants, variants that are neither common in the population nor evolutionarily informative39–41. to identify these variants, we first used haplogrep to determine the haplogroup of each sample39. from the constitutional variants, we removed variants that were accounted for by the sample haplogroup (global variants) as well as mutational […]

2017
PMCID: 5299762
PMID: 28178941
DOI: 10.1186/s12864-017-3539-3

[…] were compared in order to calculate ndna versus mtdna distance-differences., for both the 1kgp and the hgdp data, mitochondrial haplotypes were determined from mtdna sequence variants using the haplogrep2 program [41]. evolutionary relationships among mtdna haplogroups were taken from the phylotreemt website [42]. counts of mtdna haplogroups were determined for the individual populations, […]

2017
PMCID: 5335606
PMID: 28256601
DOI: 10.1038/srep42869

[…] and in supplementary table s11., consensus sequences were called using samtools packages73: only high quality calls with a quality score of 30 or more were kept. the two sequences were uploaded on haplogrep4849 to assign the mitochondrial genome to known haplogroups and call mtdna snps, followed by manual verification of each diagnostic variant., in order to reduce the loss of the information, […]

2017
PMCID: 5483232
PMID: 28552360
DOI: 10.1016/j.cub.2017.05.023

[…] as well as variants called at the last 4 bases of any of the two read ends were excluded from further analysis, as they could have resulted from molecular damage. haplogroup assignment was based on haplogrep (http://haplogrep.uibk.ac.at/) (table s4)., all our three male samples, sc1_meso, sc2_meso and oc1_meso, were assigned to the r1 and r1b haplogroups (table 1 in main text) using yfitter, […]

2017
PMCID: 5483232
PMID: 28552360
DOI: 10.1016/j.cub.2017.05.023

[…] called at the last 4 bases of any of the two read ends were excluded from further analysis, as they could have resulted from molecular damage. haplogroup assignment was based on haplogrep (http://haplogrep.uibk.ac.at/) (table s4)., all our three male samples, sc1_meso, sc2_meso and oc1_meso, were assigned to the r1 and r1b haplogroups (table 1 in main text) using yfitter, a maximum likelihood […]

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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