VarDict protocols

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chevron_left Indel detection Duplication detection SNV detection Variant detection Inversion detection Deletion detection chevron_right
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VarDict specifications

Information


Unique identifier OMICS_11609
Name VarDict
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data VarDict works on Binary Alignment/Map (BAM) files that contain aligned sequence reads against a reference genome.
Operating system Unix/Linux
Programming languages Perl
License MIT License
Computer skills Advanced
Stability Stable
Requirements
R, samtools
Maintained Yes

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  • person_outline Zhongwu Lai <>

Publication for VarDict

VarDict in pipelines

 (5)
2017
PMCID: 5324109
PMID: 28233799
DOI: 10.1038/srep43169

[…] number of reads containing the alternate allele (#alt), the depth (dp) and the variant allele frequency (vaf) was determined using r (http://www.r-project.org). some variant callers, like gatk or vardict, automatically perform local realignment when calling variants. as this rearrangement of the reads can lead to changes in #ref, #alt, dp and vaf, the raw bam files resulting […]

2017
PMCID: 5564797
PMID: 28572531
DOI: 10.18632/oncotarget.17913

[…] cfdna samples and ∼2800× for the genomic dna from whole blood., bwa [] was employed for mapping the pair-end reads to human reference genome hg19, samblaster [] for marking duplicate reads, and vardict [] for detection of single nucleotide variants (snvs) and small insertions and deletions (indels). snvs and small indels were called with the criteria of allele frequency ≥ 0.5% and at least […]

2017
PMCID: 5725088
PMID: 29245897
DOI: 10.18632/oncotarget.18502

[…] hg19 human reference genome assembly using bwa [], no realignment or recalibration was performed. duplicate reads were removed from final bam files using samblaster []. variants were called using vardict [], with thresholds of minimal allowed read support of 3, minimal mean position in reads of 5, minimal mean base quality phred score of 25, and minimal mean mapping quality score of 10., […]

2017
PMCID: 5739687
PMID: 29285300
DOI: 10.18632/oncotarget.22413

[…] software (https://broadinstitute.github.io/picard/). the base recalibration and indel realignment were processed using the gatk [] (version 3.6) package. somatic point mutations were called with vardict [] algorithms. copy number variations (cnvs) were detected with cnvkit []. the exome sequencing data analysis was implemented by bcbio_nextgen (https://github.com/chapmanb/bcbio-nextgen) […]

2016
PMCID: 5342331
PMID: 27472462
DOI: 10.18632/oncotarget.10852

[…] sequences were then filtered from human alignment before downstream analysis. expression was quantified into rpkm using and rseqc. variants from rna-seq were called by an in-house variant caller vardict. mutations were identified after filtering common snps and non-functional variants, such as silent and those in utr or introns., tumors and lungs immunohistochemistry was performed using […]


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VarDict in publications

 (21)
PMCID: 5944071
PMID: 29743009
DOI: 10.1186/s12864-018-4753-3

[…] in experiments likely to be analyzed using muver. to provide context for these values, we identified clonal differences with varscan version 2.4.3 [] using the somatic mutation calling workflow and vardict version 1.5.1 []. additionally, we called variants with haplotypecaller for the father and son individually, and combined the results to identify differences., muver analyses were performed […]

PMCID: 5943456
PMID: 29743479
DOI: 10.1038/s41467-018-04283-9

[…] analysis pipeline was used for data processing and variant calling. briefly, reads were aligned against the reference genome (grch38) using bwa-mem and variants were called using two methods (vardict and gatk haplotypecaller). consensus variants and their effects on crispr clones were then calculated. all clones used in this paper were str genotyped and confirmed as free from mycoplasma., […]

PMCID: 5906695
PMID: 29670109
DOI: 10.1038/s41467-018-03828-2

[…] genome (hg19) using bwa. duplicated reads marked by picard were removed. indel regions were realigned using gatk. somatic mutations were called by four independent mutation callers: varscan, mutect, vardict, and freebayes using default parameters of the bcbio-nextgen pipeline. as the nature of our analyses requires high specificity in somatic mutation calling, we developed a random forest […]

PMCID: 5901877
PMID: 29661213
DOI: 10.1186/s13073-018-0537-2

[…] around indels, and removing pcr duplicates. raw single-nucleotide variant (snv) calls for the bulk datasets were obtained using the paired-sample variant-calling approach implemented in the vardict software []. for the n8 dataset, since samples from both primary tumor and metastasis were available, vardict was run twice, independently for both samples, and the resulting snvs […]

PMCID: 5852328
PMID: 29552334
DOI: 10.1016/j.csbj.2018.01.003

[…] by most snv callers, a read can be included at one position and excluded at another, depending on the base quality scores at each individual position. some variant callers such as strelka  and vardict  implement local indel realignments during pre-processing, resulting in better accuracy around indels. this can also be done using gatk indelrealigner and bqsr (base quality score […]


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VarDict institution(s)
Oncology iMed, AstraZeneca, Waltham, MA, USA; Oncology iMed, AstraZeneca, Cambridge, UK; Bioinformatics Core, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Bearsden Glasgow, UK
VarDict funding source(s)
Supported by AstraZeneca.

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