HaploPainter protocols

HaploPainter specifications


Unique identifier OMICS_00209
Name HaploPainter
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format pedigree, haplotypes, map file
Operating system Unix/Linux, Mac OS, Windows
Programming languages Perl
Computer skills Advanced
Stability Stable
Requirements GTK+, Cairo, Glib
Maintained Yes



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  • person_outline Holger Thiele <>

Publication for HaploPainter

HaploPainter IN pipelines

PMCID: 5916965
PMID: 29725345
DOI: 10.3389/fgene.2018.00133

[…] large pedigree of 23 generations. however, due to the linkage software restraints, the cases were clustered into 27 smaller (≤24 bits) families using pedcut software (liu et al., 2008). we used haplopainter (thiele and nürnberg, 2005) to illustrate all 27 pedigrees (supplementary figure s1). we then performed affected-only parametric linkage analysis in merlin software (abecasis et al., […]

PMCID: 4144801
PMID: 25157627
DOI: 10.1371/journal.pone.0104496

[…] analyses in family i to determine the locus that co-segregates with the disease. maximal lod score of 1.5 was obtained on chromosome 8 and 20 (figure s2). haplotype co-segregation analyses by haplopainter [9] mapped the linkage critical region to chr20: 17,722,478–36,009,145. there are 165 snps in chromosome 20 for linkage analysis after ld pruning., sequence reads were mapped by bwa [18] […]

HaploPainter institution(s)
Gene Mapping Center, Max Delbrueck Center (MDC) for Molecular Medicine Berlin-Buch, Berlin, Germany; Institute of Medical Genetics, University Medicine of Berlin, Berlin, Germany; Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
HaploPainter funding source(s)
This work was funded by the Federal Ministry of Science and Education of Germany through the National Genome Research Network.

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