readDepth protocols

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chevron_left Duplication detection Deletion detection Somatic CNA detection CNV detection chevron_right
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readDepth specifications

Information


Unique identifier OMICS_00350
Name readDepth
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format BED
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License Apache License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for readDepth

readDepth in pipelines

 (2)
2015
PMCID: 4485032
PMID: 26122179
DOI: 10.1038/srep11711

[…] the burrow-wheeler-aligner (bwa) v0.7.5a algorithm and non-uniquely mapping reads were removed with samtools v0.1.19 and bedtools v2.17.0. cna detection was performed using the bioinformatics tool readdepth, which performed best in a recent comparison of different cna detection methods. for this, the genome sequence was divided into non-overlapping windows or bins of 1 mb in size […]

2013
PMCID: 3604020
PMID: 23527109
DOI: 10.1371/journal.pone.0059128

[…] required. the normalized read depth signal is processed following one of the two ways: (1) first segmented by local change-point (or segmentation, partition) algorithms and a merge procedure (e.g. readdepth uses circular binary segmentation (cbs); cnvnator uses mean shift; and freec uses lasso based method); (2) tested by a statistical hypothesis at each window (e.g. event-wise testing […]

readDepth in publications

 (12)
PMCID: 5432334
PMID: 28460482
DOI: 10.18632/oncotarget.15932

[…] []. additional bioinformatics tools are needed to more precisely estimate cnas from wes data., several tools have been developed for estimating somatic cnas using ngs data. for example, cnv-seq, readdepth, cnvnator, and hmmcopy use wgs data, and exomecnv, varscan2, convex, codex, conifer, and exome2cnv use wes data as inputs. control_freec, saascnv, ngcgh, and falcon use both wgs and wes [, […]

PMCID: 4938731
PMID: 27270588
DOI: 10.1038/nm.4120

[…] genes in the tumors, mutation calls with less than 20 reads were excluded. r and bioconductor packages were used to prioritize and visualize the sequencing data. the segment plotting tool from the readdepth package for r was further modified to visualize cnv alterations. the sequencing data have been deposited in the national center for biotechnology information (ncbi) database of genotypes […]

PMCID: 4632076
PMID: 26534864
DOI: 10.1038/srep16106

[…] and details., to detect maternal cnv, chromosomes were divided into 100-kb window bins prior to obtaining the count statistics; adjacent window bins shared a 50% area of overlap. similar to various readdepth-based algorithms, the number of unique mapped reads in each window bin was counted, adjusted in terms of gc bias and mapability ratio, and then converted to a window bin z-score […]

PMCID: 4570720
PMID: 26374103
DOI: 10.1186/s40246-015-0044-0

[…] a tumor sample and its matched normal sample. these methods can be further categorized according to the study design. some commonly used ones are as follows. (a) cnvnator [], rdxplorer [], and readdepth [] detect cnas on a single tumor sample. (b) cnaseg [], segseq [], exomecnv [], hmmcopy [], and varscan2 [] identify cnas on matched tumor-normal samples. control-freec [, ] […]

PMCID: 4485032
PMID: 26122179
DOI: 10.1038/srep11711

[…] methods, the variability in distribution of the reads across the genome and the ability to correctly detect chromosomal aneuploidies and large cnas was compared using the bioinformatics tool readdepth. the final mps results were compared to a 180 k arraycgh profile (agilent technologies) of genomic dna of the loucy cell line which was determined prior to the experiments to serve […]

readDepth institution(s)
Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX, USA

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