GenomeComb protocols

View GenomeComb computational protocol

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GenomeComb specifications

Information


Unique identifier OMICS_19324
Name GenomeComb
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data Some sequencing data from Complete Genomics, Illumina, SOLiD and VCF.
Output data A standard file format used is a simple tab delimited file.
Output format SFT, TSV
Operating system Unix/Linux
License GNU General Public License version 3.0
Computer skills Advanced
Version 0.90.0
Stability Stable
Maintained Yes

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Documentation


Maintainer


  • person_outline Albena Jordanova <>

Publications for GenomeComb

GenomeComb in pipelines

 (2)
2016
PMCID: 4947104
PMID: 27026413
DOI: 10.1007/s00401-016-1566-9

[…] and mapping was done against whole reference genome hg19 using the burrows–wheeler aligner []. variant calling and annotation was performed using gatk version 2.2 [] and annotated using the genomecomb software pipeline []. variants with a read depth below 20 reads or with an imbalanced reference/variant allele read depth exceeding 3:1 were considered false calls. all remaining variants […]

2015
PMCID: 4693503
PMID: 26613940
DOI: 10.15252/emmm.201505323

[…] , dbsnp, http://www.ncbi.nlm.nih.gov/projects/snp , exac browser, http://exac.broadinstitute.org , genome analysis toolkit (gatk) unified genotyper, https://www.broadinstitute.org/gatk , genomecomb, http://genomecomb.sourceforge.net , multiplex amplification of specific targets for resequencing (mastr), […]


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GenomeComb in publications

 (8)
PMCID: 5563332
PMID: 28447221
DOI: 10.1007/s00401-017-1714-x

[…] was performed with fastq-mcf [], aligned with burrows-wheeler aligner memv0.7.5a [] and variants were called with gatkv2.4 unifiedgenotyper and gatkv3.5 haplotypecaller. variants were annotated with genomecomb [] and snpeff []., for four exons (12, 17, 19, and 23), no compatible primers were found. exons 12, 17, and 19 were analyzed with sanger sequencing: exons were pcr amplified, subsequently […]

PMCID: 4947104
PMID: 27026413
DOI: 10.1007/s00401-016-1566-9

[…] and mapping was done against whole reference genome hg19 using the burrows–wheeler aligner []. variant calling and annotation was performed using gatk version 2.2 [] and annotated using the genomecomb software pipeline []. variants with a read depth below 20 reads or with an imbalanced reference/variant allele read depth exceeding 3:1 were considered false calls. all remaining variants […]

PMCID: 4695081
PMID: 26714269
DOI: 10.1371/journal.pone.0144428

[…] per seven samples prior to amplification, patient samples were amplified individually. libraries were sequenced on miseq (illumina, ca, usa) using v3 chemistry. after performing filtering steps in genomecomb [] (), remaining variants were tested for association with the schizophrenic or epileptic phenotype using a two-sided fisher’s exact test. all variants with p < 0.05 were subsequently […]

PMCID: 4693503
PMID: 26613940
DOI: 10.15252/emmm.201505323

[…] recessive model. hereto, variants were called using genome analysis toolkit (gatk) unified genotyper (mckenna et al, ) and samtools (li et al, ). for the downstream analysis of the variants, we used genomecomb (reumers et al, ), an in‐house developed tool for the annotation and filtering of ngs data. the dataset was further filtered using the following criteria: (i) read depth in all individuals […]

PMCID: 4641381
PMID: 26555887
DOI: 10.1186/s40478-015-0246-7

[…] reads against the human genome reference sequence hg19 were performed with the burrows-wheeler aligner []. variant calling and annotation were performed using gatk (version 2.2) in combination with genomecomb software [, ]. identified variants were independently validated using direct sanger sequencing on genomic dna. flnc codon numbering was based on genbank accession number nm_001458.4 […]


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GenomeComb institution(s)
Molecular Neurogenomics Group, Department of Molecular Genetics, VIB, University of Antwerp, Antwerp, Belgium; Neurogenetics Laboratory, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium; Department of Medical Chemistry and Biochemistry, Molecular Medicine Center, Medical University-Sofia, Sofia, Bulgaria; Department of Molecular Genetics, VIB, University of Antwerp, Antwerp, Belgium; Department of Neurology, Medical University-Sofia, Sofia, Bulgaria; Department of Pediatrics, Dicle University School of Medicine, Diyarbakir, Turkey; Department of Neurological, Neuropsychological, Morphological and Motor Sciences, University of Verona, Verona, Italy; Division of Pediatric Neurology, Department of Pediatrics, Faculty of Medicine, Hacettepe University, Ankara, Turkey; Department of Cognitive Science and Psychology, New Bulgarian University, Sofia, Bulgaria; Department of Neurology, Istanbul Medical Faculty, Istanbul University, Istanbul, Turkey; Department of Molecular Biology and Genetics, Bogazici University, Istanbul, Turkey
GenomeComb funding source(s)
Supported in part by the University of Antwerp (TOP BOF 29069); the Fund for Scientific Research–Flanders, Tom Wahlig Foundation, Jena, Germany; and the Bogazici University Research Fund (11B01P7); by fellowships from the Fund for Scientific Research–Flanders and by a travel grant from the Boehringer Ingelheim Fonds, Germany.

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