ERDS pipeline

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 IN pipelines

 (4)
2017
PMCID: 5438018
PMID: 28221368
DOI: 10.1038/tp.2016.258

[…] respectively. the minimum number of independent reads required for variant calling was set at 4. snv and indels were then collected in a unique vcf file and annotated using the annovar package.13, erds software was used to infer cnvs (http://www.utahresearch.org/mingfuzhu/erds/).14, all association tests performed were based on fisher's exact test with bonferroni correction for multiple […]

2017
PMCID: 5510834
PMID: 28708842
DOI: 10.1371/journal.pone.0179924

[…] accessed from the university of california, santa cruz (ucsc) genome browser (https://genome.ucsc.edu/). (see s3 table for gaers- and s4 table for nec-specific protein-coding indels)., we used the estimation by read depth with single-nucleotide variants (erds) platform, based on read depth and paired-end mapping data [34] to identify copy number variants (cnvs) among the gaers and nec sequence […]

2017
PMCID: 5510834
PMID: 28708842
DOI: 10.1371/journal.pone.0179924

[…] genome browser (https://genome.ucsc.edu/). (see s3 table for gaers- and s4 table for nec-specific protein-coding indels)., we used the estimation by read depth with single-nucleotide variants (erds) platform, based on read depth and paired-end mapping data [34] to identify copy number variants (cnvs) among the gaers and nec sequence data. to qualify, cnv calls by erds were required […]

2017
PMCID: 5510834
PMID: 28708842
DOI: 10.1371/journal.pone.0179924

[…] variants (erds) platform, based on read depth and paired-end mapping data [34] to identify copy number variants (cnvs) among the gaers and nec sequence data. to qualify, cnv calls by erds were required to be ≥5000bps and to result in either complete loss of sequence (for deletions) or at least 2-fold increase in instance (for duplications). as a result, 354 and 475 putative […]

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

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