DELLY pipeline

DELLY specifications

Information


Unique identifier OMICS_00313
Name DELLY
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for DELLY

DELLY IN pipelines

 (8)
2017
PMCID: 5617183
PMID: 28953922
DOI: 10.1371/journal.pone.0185103

[…] best practices [10, 11]variants were called using haplotype caller (gatk) [12] and platypus[13]. structural variants (big deletion or insertions among the amplified fragments) were called with delly2[14]. the resulting vcf files were annotated with structural information with snpeff [15] to detect variations with moderate or high impact. allelic frequency was calculated considering […]

2016
PMCID: 4843186
PMID: 26884591
DOI: 10.1093/annonc/mdw042

[…] human genome (hg19) using the burrows-wheeler alignment tool. duplicates are then filtered using the picard-tools java package (samtools) and searched for candidate structural rearrangements using delly. all candidate somatic structural aberrations were filtered, annotated using in-house tools, and manually reviewed using the integrative genomics viewer., the facets algorithm was used […]

2016
PMCID: 5248613
PMID: 27461929
DOI: 10.1111/age.12465

[…] a length of more than 1 kb that were identified in at least one sample and were not of the amphiploid form were retained for further analysis. to identify long insertions and deletions, we performed delly (ver 0.5.9) (rausch et al. 2012) using paired mapping data and the following criteria: more than three paired‐end supports, a length between 300 bp and 1000 bp, and a mapq (mapping quality) […]

2016
PMCID: 5521736
PMID: 28173099
DOI: 10.1093/gbe/evw286

[…] 0.05/(g − 1), where g equals 8,171—the total number of genes in the genome., using the bam files for all ma lines from the above pipelines, we analyzed the presence of structural variants using the delly software package (workflow available on github, https://github.com/behrimg/r_toruloides) (rausch et al. 2012). for structural variants present on the shorter contigs (contigs 49–94), variants […]

2015
PMCID: 4313365
PMID: 25533785
DOI: 10.1016/j.cell.2014.11.050

[…] burrows-wheeler aligner (bwa) 0.7.5a with settings ‘bwa mem -c 100 -m’ resulting in sample-specific bam files. to predict cnvs, bam files were analyzed using control-freec (boeva et al., 2012) and delly (rausch et al., 2012). to obtain somatically acquired cnvs, we filtered called cnvs for occurrence in the reference samples (liver biopsies). single nucleotide variants (snvs) […]

DELLY institution(s)
European Molecular Biology Laboratory, Genome Biology, Heidelberg, Germany

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