SimWalk2 protocols

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SimWalk2 statistics

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Associated diseases

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SimWalk2 specifications

Information


Unique identifier OMICS_09408
Name SimWalk2
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Fortran
Computer skills Advanced
Version 2.91
Stability Stable
Maintained No

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Publications for SimWalk2

SimWalk2 in pipeline

2009
PMCID: 2747327
PMID: 19229252
DOI: 10.1038/jhg.2009.2

[…] because analyses carried out with potentially incorrect allele frequencies (e.g. equal allele frequencies) can increase type i error (). haplotypes in the 8p22-21.3 region were reconstructed using simwalk2., primers were designed for the exons of the hairless (hr) gene (mim 602302) isoform a (nm_005144) and isoform b (nm_018411), the platelet-derived growth factor receptor-like (pdgfl) gene […]


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SimWalk2 in publications

 (82)
PMCID: 5821217
PMID: 29367466
DOI: 10.1172/jci.insight.98555

[…] icr at a density of 20 cm were selected from the genome. seventy-two p0 newborns from 8 litters with 11 chd cases and thirty-eight e9.5 embryos from 3 litters with 6 chd cases were genotyped. using simwalk2, which contains block statistics and is the most powerful method to detect linkage in a recessive model, a significant linkage on chromosome 15 at 60 cm was detected with –log(p) = 4 […]

PMCID: 5901503
PMID: 29384555
DOI: 10.1590/1678-4685-GMB-2016-0162

[…] respective microsatellite markers. markers used in the genotyping were arranged according to rutgers combined linkage-physical map (build 36.2) of the human genome (). haplotypes were analyzed by simwalk2 ()., primers used for pcr amplification, sequencing and coding of intron-exon junctions of the wnt10b gene were the same as described earlier (). the pcr-amplified products were purified […]

PMCID: 5510992
PMID: 28715588
DOI: 10.1167/iovs.16-21271

[…] each family was analyzed individually, and afterward, cumulative lod scores and hlod scores were calculated across all families., multipoint analyses were performed using simwalk2.– previous studies have shown that multipoint linkage using a dense marker map with strong intermarker ld often lead to type i error inflation, so we pruned the data by condensing snps […]

PMCID: 5473749
PMID: 28592650
DOI: 10.1534/g3.117.041764

[…] including random effect terms., the variance component approach requires ibd kinship matrices as variance-covariance matrices for testing qtl effects at each genetic position. ibd analyses using simwalk2 software () were conducted to estimate the ibd matrices formed by empirical kinship coefficients for each pair of eg9pp individuals and their parents. simwalk2 implements a bayesian […]

PMCID: 5333839
PMID: 28253278
DOI: 10.1371/journal.pone.0172807

[…] errors prior to analysis. there are no hard and fast rules about how to clean genotyping errors from pedigree data. researchers, typically, clean their data using: pedcheck [], merlin [], mendel [], simwalk2 [], or sibmed []., at the center of inherited disease research (cidr), to deal with their large-scale data flow; they formalized their data cleaning approach in a set of rules, […]


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SimWalk2 institution(s)
Department of Human Genetics, University of California, Los Angeles, Calif, USA; Centre National de Génotypage, Paris, France; Department of Human Genetics, University of Pittsburgh, PA, USA

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