LDlink protocols

LDlink specifications

Information


Unique identifier OMICS_09139
Name LDlink
Alternative name nci-webtools-dceg-linkage
Interface Web user interface
Restrictions to use None
Computer skills Basic
Version 3.0
Stability Beta
Maintained Yes

Subtools


  • LDassoc
  • LDhap
  • LDmatrix
  • LDpair
  • LDproxy
  • SNPchip
  • SNPclip

Maintainer


  • person_outline Mitchell J. Machiela <>

Additional information


https://analysistools.nci.nih.gov/LDlink/?tab=help

Information


Unique identifier OMICS_09139
Name LDlink
Alternative name nci-webtools-dceg-linkage
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Javascript, Python, Shell (Bash), Other
Computer skills Advanced
Version LDlink_2.0_10042016
Stability Stable
Maintained Yes

Subtools


  • LDassoc
  • LDhap
  • LDmatrix
  • LDpair
  • LDproxy
  • SNPchip
  • SNPclip

Download


Versioning


Add your version

Maintainer


  • person_outline Mitchell J. Machiela <>

Additional information


https://analysistools.nci.nih.gov/LDlink/?tab=help

Publications for LDlink

LDlink IN pipelines

 (6)
2018
PMCID: 5813894
PMID: 29447163
DOI: 10.1371/journal.pgen.1007194

[…] data on the quantile normalized huex array were downloaded from the gdac firehose (https://gdac.broadinstitute.org/) and cbioportal’s normalized rnaseq z-scores., we examined snp-based linkage via ldlink, ldproxy [47] using the ceu population for reference. the functional predictions for missense snps were scored by polyphen [22] and the regulation was scored by haploreg (v4) [48] using […]

2018
PMCID: 5879874
PMID: 29619113
DOI: 10.1186/s12263-018-0597-3

[…] genomic inflation factors (gif) were estimated for the two pqtl analyses using estlambda function available in the genabel r package [21]. pairwise linkage disequilibrium (ld) was calculated with ldlink, a web-based application using 1000 genome phase 3 data [22]., association between circulating angptl3 and clinical variables (bmi, fasting glucose and insulin levels, total lipid levels, […]

2017
PMCID: 5328407
PMID: 28187197
DOI: 10.1371/journal.pgen.1006587

[…] giving a total of 127,594 snps. these were then overlapped with the t-bet binding sites. to identify the number of independent ld blocks were represented by the 926 t-bet bound snps, we used the snpclip module of ldlink to reduce any snps in high ld to a single tag snp, using a r2 threshold of 0.8 and a maf (minimum allele frequency) threshold of 0.01., chip-seq data for igg, h3k27ac […]

2017
PMCID: 5328407
PMID: 28187197
DOI: 10.1371/journal.pgen.1006587

[…] of 127,594 snps. these were then overlapped with the t-bet binding sites. to identify the number of independent ld blocks were represented by the 926 t-bet bound snps, we used the snpclip module of ldlink to reduce any snps in high ld to a single tag snp, using a r2 threshold of 0.8 and a maf (minimum allele frequency) threshold of 0.01., chip-seq data for igg, h3k27ac and total h3 were taken […]

2016
PMCID: 4766752
PMID: 26911590
DOI: 10.1186/s12864-016-2481-0

[…] of 2.14 × 10−06 for 23,390 gene tests was used, with suggestive significance set at 1 × 10−05., analysis of the linkage disequilibrium (ld) surrounding variants of interest was performed using ldlink (1000 genomes project phase 3 eur population) [37]. prediction of histone marks, dnase hypersensitivity sites and expression quantitative trait locus (eqtl) associations was performed using […]

LDlink institution(s)
Division of Cancer Epidemiology and Genetics, National Cancer Institute, Chinakville, MD
LDlink funding source(s)
Support comes from the Division of Cancer Epidemiology and Genetics Informatics Tool Challenge.

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