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This repo has migrated to GitLab

https://gitlab.com/mtekman/HaploForge

(The copy here is archived. Please see the above link for the latest developments)

HaploForge

A Comprehensive Pedigree Drawing and Haplotype Visualisation Web Application
  • Creates pedigrees and imports/exports them using LINKAGE format.
  • Renders haplotypes for popular haplotyping/linkage programs such as Allegro, Merlin, Genehunter, and Simwalk.
  • Resolves haplotypes using a novel A*-search based approach for autosomal and X-linked disease models, both recessive and dominant.
  • Performs identity mapping for homozygous, heterozygous, and compound heterozygous disease models.
  • Can auto-generate large and complex pedigrees via meioses simulation benchmarks.

HaploForge is licensed under the GPLv3.

If HaploForge is used to analyse your work, please cite Tekman et al, 2017.

@article{Tekman2017,
    author = {Tekman, Mehmet and Medlar, Alan and Mozere, Monika and Kleta, Robert and Stanescu, Horia},
    title = {HaploForge: a comprehensive pedigree drawing and haplotype visualization web application},
    journal = {Bioinformatics},
    volume = {33},
    number = {24},
    pages = {3871-3877},
    year = {2017},
    doi = {10.1093/bioinformatics/btx510},
    URL = { + http://dx.doi.org/10.1093/bioinformatics/btx510},
    eprint = {/oup/backfile/content_public/journal/bioinformatics/33/24/10.1093_bioinformatics_btx510/1/btx510.pdf}
}

The live web application is hosted here

dos2.png

How are haplotypes phased?

Haplotype applications output two types of files: phased genotypes, and vectors.

Phased genotypes encode the maternal and paternal alleles for an individual, but do not record founder allele mapping.

Vector files describe the flow of genetic information from one generation to the next. This can be encoded either by recording the founder allele at each individual-marker, or by recording where each recombination/crossover event took place.

HaploForge by default makes of it's own novel A*-search based algorithm to find these recombination points and determine the founder allele mapping, but also optionally makes use of vector output.

Why is this better than HaploPainter?

  • It's on the web, no need for extensive Perl installations
  • It's current, with active development since 2014
  • X-linked resolver, something that HaploPainter did not correctly implement.

How to use?

Simply go to the live application and go through the quick video tutorials (in total no longer than 10 minutes).

Can I install HaploForge locally?

Yes, though there will be no performance benefit since HaploForge processess all data within the client web browser.

However, there is a helper script availiable in this regard:

helpers/public/generate_public.sh

Simply run this (examples provided in help text) to generate a public webpage and then host it using your preferred hosting software (e.g. apache2, nginx, lighttpd).

NOTE: Family names and Sample IDs must be numeric