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Merlin specifications


Unique identifier OMICS_09404
Name Merlin
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux
Programming languages C++
Computer skills Advanced
Version 1.1.2
Stability Stable
Maintained Yes


No version available


  • person_outline Gonçalo Abecasis

Publication for Merlin

Merlin citations


Cross ancestry genome wide association analysis of corneal thickness strengthens link between complex and Mendelian eye diseases

Nat Commun
PMCID: 5951816
PMID: 29760442
DOI: 10.1038/s41467-018-03646-6

[…] first five principle components for the population-based studies. In samples with related individuals association testing accounting for family structure was conducted using the –fastAssoc option in MERLIN or the –mmscore option implemented in GenABEL. Before meta-analysis, we removed variants with MAF < 0.01, and with imputation quality scores less than 0.3.Ancestry specific meta-analyses (Europ […]


Family Based Genome Wide Association Study of South Indian Pedigrees Supports WNT7B as a Central Corneal Thickness Locus

PMCID: 5961220
DOI: 10.1167/iovs.17-23536

[…] tion of ranks was applied to CCT measurements before analysis. Age and sex were included as covariates in the association tests. The genome-wide association test was performed using the score test in MERLIN (v1.1.2, provided in the public domain,,, which incorporated genetic relatedness based on the family structure. Because this program applies a restri […]


An epistatic effect of KRT25 on SP6 is involved in curly coat in horses

Sci Rep
PMCID: 5913262
PMID: 29686323
DOI: 10.1038/s41598-018-24865-3

[…] agment length polymorphisms (RFLP) for the remaining five variants in 148 curly coated and 68 straight coated horses (Supplementary Table ). Graphic representation of haplotypes was constructed using Merlin and Haplopainter. For the SP6 variant a mismatch primer was used according to. The three variants, whose genotypes segregated with the phenotypes, NC_009154.2:g.21891160G>A (KRT25), NC_009154.2 […]


A Genome Wide Linkage Study for Chronic Obstructive Pulmonary Disease in a Dutch Genetic Isolate Identifies Novel Rare Candidate Variants

Front Genet
PMCID: 5916965
PMID: 29725345
DOI: 10.3389/fgene.2018.00133
call_split See protocol

[…] 27 smaller (≤24 bits) families using PEDCUT software (). We used HaploPainter () to illustrate all 27 pedigrees (Supplementary Figure ). We then performed affected-only parametric linkage analysis in MERLIN software () using incomplete penetrance and no phenocopies for both dominant (0, 0.5, 0.5) and recessive models (0, 0, 0.5) (). The measure of the likelihood of linkage is the LOD score and we […]


Combined linkage and association analysis of classical Hodgkin lymphoma

PMCID: 5945548
PMID: 29755658
DOI: 10.18632/oncotarget.24872
call_split See protocol

[…] . Mendelian errors were removed and SNPs with high heterozygosity spaced ∼0.3Mb apart selected using linkdatagen were used for linkage analysis []. Non-parametric linkage analysis was performed using MERLIN [].Typing of classical HLA alleles was performed using SeCore sequencing (Life Technologies, UK) in conjunction with Applied Biosystems 3130XL technology and analysed using uTYPE 6.0 software ( […]


Rare ABCA7 variants in 2 German families with Alzheimer disease

PMCID: 5863691
PMID: 29577078
DOI: 10.1212/NXG.0000000000000224

[…] A set of 2,000 variants per chromosome along with the identified variants segregating with the disease through the pedigree were used to check for genotype errors and mendelian inconsistencies using MERLIN and were subsequently removed if they were identified as errors. The remaining variants were used for linkage analysis and their genomic positions were linearly interpolated based on the hapmap […]


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Merlin institution(s)
The Wellcome Trust Center for Human Genetics, University of Oxford, Oxford, UK

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