LDlink specifications

Information


Unique identifier OMICS_09139
Name LDlink
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
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

LDlink articles

LDlink citations

 (3)
2018
PMCID: 5813894

[…] 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 […]

2017
PMCID: 5328407

[…] 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 […]

2015
PMCID: 4581478

[…] 39) are located ~177 kb apart and are not in strong linkage disequilibrium (ld) in individuals of european or american descent (r2 = 0.15 and r2 = 0.12, respectively, http://analysistools.nci.nih.gov/ldlink/). the two variants were genotyped in three distinct cohorts of hesn and geographically matched hiv-1 sp subjects (table 1). the main risk factor in all hesn was unprotected sex.table 1characte […]

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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