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CODOC specifications

Information


Unique identifier OMICS_04175
Name CODOC
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Input format BAM
Operating system Unix/Linux
Programming languages Java, R
Computer skills Advanced
Version 0.0.2
Stability Stable
Maintained Yes

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Publication for CODOC

CODOC in publications

 (2)
PMCID: 4570706
PMID: 26371761
DOI: 10.1371/journal.ppat.1005160

[…] increase or decrease). we also extracted strand-specific, normalized depth-of-coverage signals (i.e., the counts of reads overlapping a particular genomic position) from the read alignments using codoc [] and converted them to the bigwig data format to enable manual inspection in a genome browser., we thank christian eggers for critical reading of the manuscript and jim driver for assistance […]

PMCID: 4459391
PMID: 25855803
DOI: 10.1093/hmg/ddv117

[…] variants were called with platypus version 0.5.2 () (www.well.ox.ac.uk/platypus) with default settings except for minflank = 0. coverage was calculated on deduplicated bam files using bedtools and codoc (). variant calling was performed across all five bam files simultaneously, producing a multi-sample vcf. the wes data from the family were extensively examined in ingenuity variant analysis […]

CODOC institution(s)
Center for Integrative Bioinformatics Vienna (CIBIV), Max F Perutz Laboratories, University of Vienna and Medical University of Vienna, Vienna, Austria
CODOC funding source(s)
Supported by the CIBIV household budget.

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