MOLGENIS Research protocols

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chevron_left eQTL mapping Read quality control Genome visualization Workflow management systems SNP/SNV annotation Protein database search chevron_right
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Associated diseases

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MOLGENIS Research specifications


Unique identifier OMICS_31543
Name MOLGENIS Research
Alternative name MOLGENIS
Interface Web user interface
Restrictions to use None
Programming languages Java, Javascript
Database management system PostgreSQL
Computer skills Basic
Version 7.1.0
Stability Stable
Maintained Yes




  • person_outline Morris Swertz <>

Additional information

Publication for MOLGENIS Research

MOLGENIS Research in pipeline

PMCID: 5352142
PMID: 28248954
DOI: 10.1371/journal.pgen.1006643

[…] eqtl mapping as described in eqtl mapping analysis cookbook developed by the university medical center groningen at the genetics department and the genomics coordination center ( and previously in []. for cis-analysis the distance between the probe midpoint and snp genomic location was up to 1 mb […]

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MOLGENIS Research in publications

PMCID: 5842149
PMID: 29531775
DOI: 10.1038/hgv.2018.6

[…] mutations; 8% are missense mutations; and 11% are splice site mutations. currently, 581 mutations have been classified as pathogenic, whereas 93 mutations remain unclassified (chd7 database: these unclassified mutations mostly comprise missense substitutions or occur around the exon/intron junctions., […]

PMCID: 5904227
PMID: 29460007
DOI: 10.1007/s00401-018-1825-z

[…] for expression quantitative trait loci (eqtls) in 10 brain regions using the v6p gtex [] portal ( as well as in whole blood using the blood eqtl browser [] (, we examined for significant contacts between glioma risk snps and nearby genes using the hugin browser [], which is based on analysis by schmitt et al. […]

PMCID: 5796395
PMID: 29394955
DOI: 10.1186/s40246-018-0136-8

[…] snps after filtering using the higher mentioned criteria. variant allele frequencies from the genome of the netherlands (gonl) project were derived from the release 5 vcf files downloaded at, additional file 1: table s1. additional file 2: table s2. additional file 3: figure s1. additional file 4:¬†figure s2. additional […]

PMCID: 5789541
PMID: 29378630
DOI: 10.1186/s13073-018-0515-8

[…] additionally, we filtered out variants in low-complexity regions of the genome as defined by li et al. []. for comparison analyses, we downloaded variant files from the gonl consortium ( and 1000 genomes phase 3 ( and searched for the presence […]

PMCID: 5789360
PMID: 29300322
DOI: 10.3390/cancers10010010

[…] , raw reads were processed using our in-house pipeline, as described previously (24). in brief, our variant calling pipeline is based on the genome analysis toolkit (gatk) workflow and uses molgenis compute as workflow management software []. read alignment was done using burrows-wheeler aligner and gatk, using the human genome reference build grch37 with decoys from the gatk bundle […]

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MOLGENIS Research institution(s)
University of Groningen and University Medical Center Groningen, Genomics Coordination Center, Groningen, The Netherlands; University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands; University of Groningen and University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, The Netherlands
MOLGENIS Research funding source(s)
Supported by the Netherlands Organization for Scientific Research (NWO), grant number 184.033.111.

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