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Protocols

ERDS specifications

Information


Unique identifier OMICS_06978
Name ERDS
Alternative name Estimation by Read Depth with Single-nucleotide variants
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C
Computer skills Advanced
Stability No
Maintained No

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Publication for Estimation by Read Depth with Single-nucleotide variants

ERDS citations

 (9)
library_books

Improved diagnostic yield compared with targeted gene sequencing panels suggests a role for whole genome sequencing as a first tier genetic test

2017
Genet Med
PMCID: 5895460
PMID: 28771251
DOI: 10.1038/gim.2017.119

[…] script and then annotated using MitImpact19 (version 2.4, http://mitimpact.css-mendel.it/) to identify known pathogenic variants. CNVs were called, using the read-depth method, by the programs ERDS (Estimation by Read Depth with Single-Nucleotide Variants) and CNVnator, using a window size of 500 base pairs. CNV size cutoffs were 1 kb for losses and 2 kb for gains. High-quality CNVs were defined […]

library_books

Genomic diagnosis for children with intellectual disability and/or developmental delay

2017
Genome Med
PMCID: 5448144
PMID: 28554332
DOI: 10.1186/s13073-017-0433-1

[…] Copy number variants (CNVs) were called from WGS bam files using ERDS [] and read depth []. Overlapping calls with at least 90% reciprocity, less than 50% segmental duplications, and that were observed in five or fewer unaffected parents were retained and subsequen […]

call_split

Whole genome sequencing of one complex pedigree illustrates challenges with genomic medicine

2017
BMC Med Genomics
PMCID: 5322674
PMID: 28228131
DOI: 10.1186/s12920-017-0246-5
call_split See protocol

[…] umpy calls, events supported by >50 reads or less than four reads were excluded because regions of either too low or high coverage are more likely to contain biases in sequencing or alignment. Sixth, ERDS (v1.1) was used to call CNVs from the BWA-mem bam files with default settings []. Among ERDS calls with a confidence score >300, duplications with sizes < 200 Kb and deletion calls with sizes <10 […]

library_books

Genome wide variant analysis of simplex autism families with an integrative clinical bioinformatics pipeline

2015
PMCID: 4850892
PMID: 27148569
DOI: 10.1101/mcs.a000422

[…] On average, 1500 unfiltered deletions and 450 unfiltered duplications were detected by ERDS applied to the WGS data (see Methods section) for each person in the study. After filtering (see Methods section), 150 deletions and 170 duplications were found on average per person. The number […]

library_books

Comparison of Sequencing Based CNV Discovery Methods Using Monozygotic Twin Quartets

2015
PLoS One
PMCID: 4374778
PMID: 25812131
DOI: 10.1371/journal.pone.0122287

[…] alibration. The GATK DepthOfCoverage tool was used to generate quality control metrics. The mean depth of coverage was 36.9 (σ = 3.4). Indels and SNVs were called using GATK UnifiedGenotyper, because ERDS relies on the generated VCF files for CNV genotyping. For CNVer, a specific alignment was strongly recommended by the authors. Therefore, the reads were mapped to the reference using the Bowtie t […]

library_books

Towards accurate characterization of clonal heterogeneity based on structural variation

2014
BMC Bioinformatics
PMCID: 4165998
PMID: 25201439
DOI: 10.1186/1471-2105-15-299

[…] r more frequently than larger SVs. BreakDancer [] utilizes only discordant read pairs, while CREST [] and Pindel [] utilize only split-reads. Several recent tools such as GenomeSTRiP [], Delly [] and ERDS [] utilize two or more signals. However, they do not have an integrative model that simultaneously explains multiple forms of signals introduced by an SV and are geared towards identifying discre […]

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ERDS institution(s)
Center for Human Genome Variation, Duke University, Durham, NC, USA

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