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LDMAP specifications

Information


Unique identifier OMICS_31241
Name LDMAP
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data Some SNP data.
Input format TPED
Output data A LD map.
Operating system Unix/Linux
Programming languages C
Computer skills Advanced
Stability Stable
Maintained Yes

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Documentation


Maintainer


  • person_outline Reuben Pengelly

LDMAP citations

 (11)
library_books

Methionine aminopeptidase 2 is a key regulator of apoptotic like cell death in Leishmania donovani

2017
Sci Rep
PMCID: 5427942
PMID: 28273904
DOI: 10.1038/s41598-017-00186-9

[…] A putative sequence was identified for LdMAP2 from the GeneDB database with accession number LdBPK_210960.1. The coding region of full length LdMAP2 was amplified from L. donovani genomic DNA by PCR using the forward primer (LdMAP2 F: AAGA […]

call_split

Whole genome sequences are required to fully resolve the linkage disequilibrium structure of human populations

2015
BMC Genomics
PMCID: 4558963
PMID: 26335686
DOI: 10.1186/s12864-015-1854-0
call_split See protocol

[…]  0.05, SNPs with Hardy-Weinberg equilibrium deviation p-value < 0.001 [] and SNPs with > 5 % missing data. All statistical analyses were performed using R [].LD map generation was performed using the LDMAP program, with default parameters [, ]. For sample size reproducibility investigations, random subsets of the full cohort were generated and LD maps generated from the resulting dataset for three […]

library_books

The utility of low density genotyping for imputation in the Thoroughbred horse

2014
PMCID: 3930001
PMID: 24495673
DOI: 10.1186/1297-9686-46-9

[…] proxy, such that the assumption of uniformity of LD and recombination along the length of a chromosome could be removed. The proxy used was linkage disequilibrium units (LDU), as calculated using the LDMAP program described and developed by Maniatis et al. []. The theory behind the LDMAP program is based on the Malecot equation [], and is described extensively elsewhere []. An LD map for each chro […]

library_books

Critical assessment of coalescent simulators in modeling recombination hotspots in genomic sequences

2014
BMC Bioinformatics
PMCID: 3890628
PMID: 24387001
DOI: 10.1186/1471-2105-15-3

[…] fastsimcoal, there appears to be a lack of rigorous validation of hotspot detection software tools in the current literature. Popular computer programs for discovering recombination hotspots include LDMAP [], LDhot [,], LDhat 2.2 rhomap package [], Hotspotter [], and sequenceLDhot []. The widely used Haploview program [,] is also an appealing tool to visually localize recombination hotspots given […]

call_split

Association Study of the β2 Adrenergic Receptor Gene Polymorphisms and Hypertension in the Northern Han Chinese

2011
PLoS One
PMCID: 3071737
PMID: 21483652
DOI: 10.1371/journal.pone.0018590
call_split See protocol

[…] e was defined P<0.05.The presence of Hardy–Weinberg equilibrium was tested by the chi-square test for goodness of fit based on a web program (http://ihg.gsf.de/cgi-bin/hw/hwa1.pl).Construction of the LDmap and haplotype blocks within C-47T, A46G and C79G polymorphisms of the ADRB2 gene was based on genotypes and utilized Haploview software (version 4.1) (http://www.broad.mit.edu/mpg/haploview/) . […]

call_split

The rise and fall of a human recombination hot spot

2009
Nat Genet
PMCID: 2678279
PMID: 19349985
DOI: 10.1038/ng.346
call_split See protocol

[…] an DNA sequences were downloaded from Ensembl. Alu motifs were identified by BLAT searches of the human genome sequence (build 36) using the UCSC genome browser. Metric LD maps were constructed using LDMAP (http://cedar.genetics.soton.ac.uk/pub/PROGRAMS/LDMAP) and historical recombination rates were estimated by coalescent analysis using LDhat (http://www.stats.ox.ac.uk/~mcvean/LDhat/), as describ […]

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