Lep-MAP protocols

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Lep-MAP specifications

Information


Unique identifier OMICS_14862
Name Lep-MAP
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input format LINKAGE
Operating system Unix/Linux
Programming languages Java
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Pasi Rastas <>

Publications for Lep-MAP

Lep-MAP in pipelines

 (2)
2018
PMCID: 5859378
PMID: 29593780
DOI: 10.3389/fgene.2018.00082

[…] allowing for a maximum overall genotyping error of 4%. the pedigree obtained was further validated for possible erroneous assignments using fimpute ()., linkage map construction was performed using lep-map v2 (). snps with maf <0.05 in individual families and those deviating from expected mendelian segregation (p < 0.001) were excluded. linkage groups were formed using a minimum lod […]

2015
PMCID: 4558911
PMID: 26337592
DOI: 10.1186/s12711-015-0148-y

[…] or length. sas-genmod was used to test for sire and dam effects (and their interaction) on sex, using a probit link function and a binomial distribution []., the linkage map was constructed with lep-map []. snps with a minor allele frequency (maf) less than 0.05 and snps that deviated from the expected mendelian segregation (p < 0.001) were excluded. linkage groups were formed […]


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Lep-MAP in publications

 (13)
PMCID: 5914296
PMID: 29719550
DOI: 10.3389/fgene.2018.00127

[…] calling consistency was evaluated and reported for each snp (ranging from 90 to 100%, average 98%). the raw sequence data has the accession number srp130211., the linkage maps were constructed using lep-map3 software ()., first, the genotypes were converted to genotype likelihoods (posteriors) using linkage2post.awk script provided with lep-map3. then the missing parental genotypes were imputed […]

PMCID: 5937187
PMID: 29487138
DOI: 10.1534/genetics.117.300627

[…] applicable to outcrossed full-sibling (full-sib) families. recently, two software packages have been developed for performing linkage mapping in full-sib families using sequencing data. these are lep-map (, ) and highmap (), both of which address the computational problem associated with high-density maps but are not specifically designed to handle low coverage sequencing data., another […]

PMCID: 5873916
PMID: 29472307
DOI: 10.1534/g3.118.200113

[…] as good quality (‘polyhighresolution’ and ‘nominorhom’ categories), from ∼40 k putative available for c.gigas on the array, and retained for downstream analyses., linkage maps were constructed using lep-map 3 (). families used for the generation of this map were assigned using cervus () as described by , and further confirmed through the ibd module in lep-map3. putative erroneous or missing […]

PMCID: 5677171
PMID: 28963166
DOI: 10.1534/g3.117.300317

[…] package in stacks (default parameters), and snps scored in <80% of f1 samples removed. these filtering criteria produced a total of 12,961 candidate snps., linkage maps were constructed using lep-map v 2.0 (). separate sex-specific maps of female segregating and male segregating loci were constructed because of the pronounced heterochiasmy exhibited by salmonids (). pairwise estimates […]

PMCID: 5395971
PMID: 28422147
DOI: 10.1038/srep46509

[…] the flanking sequences of all 14,648 snps were listed in ., based on a double pseudo-test cross strategy, a high-density rad-based snp genetic map of m. amblycephala was first constructed using lep-map. a total of 14,648 segregating snps were successfully classified into 24 lgs (). the maternal map contained 9,531 snps with a total genetic distance of 2390.06 cm; the length of each lg […]


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Lep-MAP institution(s)
Department of Biosciences, Metapopulation Research Group, University of Helsinki, Finland; Institute of Biotechnology, University of Helsinki, Finland
Lep-MAP funding source(s)
Supported by the National Research Council of Finland (250444 and 256453) and the European Research Council (232826).

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