GenPlay protocols

GenPlay specifications

Information


Unique identifier OMICS_08292
Name GenPlay
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
License GNU General Public License version 3.0
Computer skills Medium
Stability Stable
Maintained Yes

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Documentation


Maintainers


  • person_outline Julien Lajugie <>
  • person_outline Eric Bouhassira <>

Publications for GenPlay

GenPlay IN pipelines

 (3)
2015
PMCID: 4479011
PMID: 25987481
DOI: 10.1038/ncomms8051

[…] in the user-provided reference vcf file., once the variants had been called, the vcf files for the ns library were phased using the vcf for family fny01 as a reference and specific functions in genplay multi-genome56. once the files were phased, files (in bed format) containing the allele depth for the paternal and maternal chromosomes were generated, again using specific functions provided […]

2015
PMCID: 4479011
PMID: 25987481
DOI: 10.1038/ncomms8051

[…] multi-genome56. once the files were phased, files (in bed format) containing the allele depth for the paternal and maternal chromosomes were generated, again using specific functions provided in genplay., origin usage for each of the 164,327 called peaks (origins of replication) was then computed by summing the read depth of all the snps contained in each of the peak for the two parental […]

2013
PMCID: 3669306
PMID: 23741343
DOI: 10.1371/journal.pone.0064571

[…] higher than normal read-depth in all quartet members. (more refined analysis was performed subsequently to identify cnvs). the filter was created using cnvnator and the island finder algorithm of genplay. about 18.8 * 10e6 bases, that is 0.66% of the genome (assuming a genome size of 2.86*10e9 non n bases) is covered by this filter., variant recalibration was performed following the best […]

GenPlay institution(s)
Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
GenPlay funding source(s)
Grants C024405 and C024172 from NYSTEM

GenPlay review

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Anonymous user #1933

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Desktop
Great software

Similar to IGV but much faster and a lot more functions