HaploGrep protocols

View HaploGrep computational protocol

HaploGrep statistics

To access cutting-edge analytics on consensus tools, life science contexts and associated fields, you will need to subscribe to our premium service.

Subscribe
info

Citations per year

Citations chart
info

Popular tool citations

chevron_left MtDNA haplogroup prediction chevron_right
Popular tools chart
info

Tool usage distribution map

Tool usage distribution map
info

Associated diseases

Associated diseases

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

 (14)
2018
PMCID: 5754119
PMID: 29300782
DOI: 10.1371/journal.ppat.1006750

[…] and with mapping quality less than 30 were removed using samtools []. the resulting bam files were processed using mapdamage 2.0 on default settings with plotting and statistical estimation []. haplogrep v2.1.0 [] using phylotree build 17 [] was used to identify the haplogroup of the mtdna as u5a1b. the complete genome sequence of nasd24 has been submitted to genbank and assigned accession […]

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 informative–. to identify these variants, we first used haplogrep to determine the haplogroup of each sample. 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 []. evolutionary relationships among mtdna haplogroups were taken from the phylotreemt website []. counts of mtdna haplogroups were determined for the individual populations, […]

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

[…] can be found in , and in ., consensus sequences were called using samtools packages: only high quality calls with a quality score of 30 or more were kept. the two sequences were uploaded on haplogrep 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/) ()., all our three male samples, sc1_meso, sc2_meso and oc1_meso, were assigned to the r1 and r1b haplogroups ( in main text) using yfitter, a maximum […]


To access a full list of citations, you will need to upgrade to our premium service.

HaploGrep in publications

 (95)
PMCID: 5931558
PMID: 29717136
DOI: 10.1038/s41467-018-03857-x

[…] (253 bp). for a random subset of 27 samples, new adna extracts were generated and used for a replication. in these cases, the haplogroup classification was confirmed. haplogroups were assigned with haplogrep 2.0 (http://haplogrep.uibk.ac.at/). haplogroups showing a quality score below 100% were manually re-evaluated by consulting the established mtdna phylogeny (www.phylotree.org)., […]

PMCID: 5851556
PMID: 29538439
DOI: 10.1371/journal.pone.0193578

[…] 57–357) mutational motifs and coding region polymorphic positions were inferred by comparison to the revised cambridge reference sequence (rcrs: nc_012920.1) []. haplogroups were assigned using the haplogrep2 web application, based on phylotree built 17 [, ]., for results authentication, a subset of samples (m2, m5, m9, m11, m15, m17) were independently processed in the laboratory of molecular […]

PMCID: 5844571
PMID: 29522562
DOI: 10.1371/journal.pone.0194223

[…] variants and automated indel calls were manually/visually confirmed directly from the sequences and corrected to avoid alignment errors. snps were identified and haplogroups were assigned using haplogrep 2.0 (http://haplogrep.uibk.ac.at/) [] with the assistance of mitomap (http://www.mitomap.org/mitomap) [] and phylotree (http://www.phylotree.org) []., positive and negative dna controls […]

PMCID: 5867856
PMID: 29494531
DOI: 10.3390/genes9030135

[…] the number of human sequences observed in the extraction (rb) and library preparation control (nc) samples. , the mtdna haplogroup of the final profile was determined using phylotree build 17 [] and haplogrep 2.0 []. finally, the sequence was compared to other mtdna sequences from modern and ancient populations stored in genbank, the european nucleotide archives database of the embl (ena) […]

PMCID: 5869295
PMID: 29607044
DOI: 10.1002/ece3.3924

[…] of 20 and sites with a sequencing depth of at least 5×, and at each position, a base was called only if it was observed in at least 70% of the reads covering that site (malaspinas et al., ). we used haplogrep to assign mitochondrial haplogroups of the ancient plague‐positive individuals (kloss‐brandstätter et al., )., we shotgun sequenced 14 samples representing five ancient human individuals, […]


To access a full list of publications, you will need to upgrade to our premium service.

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).

HaploGrep reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review HaploGrep