mrCaNaVaR pipeline

mrCaNaVaR specifications

Information


Unique identifier OMICS_02138
Name mrCaNaVaR
Alternative name micro-read Copy Number Variant Regions
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Input format SAM
Biological technology Illumina
Operating system Unix/Linux
Programming languages C
Computer skills Advanced
Version 0.51
Stability Stable
Maintained Yes

Versioning


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Maintainer


  • person_outline Evan E. Eichler <>

Publication for micro-read Copy Number Variant Regions

mrCaNaVaR IN pipelines

 (3)
2015
PMCID: 4676127
PMID: 26653294
DOI: 10.1186/s13059-015-0837-4

[…] 36 bp flanking each masked segment (referred to as padding regions below) were masked. the reason for the introduction of additional padding regions is that copy number variations are detected using mrcanavar [71] via the read depth in non-overlapping windows of 1 kbp of the unmasked sequence; i.e., the genomic coordinates of these windows may exceed 1 kbp, as they include masked regions. reads […]

2015
PMCID: 4712930
PMID: 26098870
DOI: 10.1038/ng.3340

[…] and tandem repeats finder 4.07b46. reads were mapped in single-read mapping mode with a hamming distance threshold of < 4 bp. we derived gc corrected absolute copy number in 100bp windows using mrcanavar version 0.5147, a program that predicts from read depth and gc enrichment an absolute copy number. we calculated a mean copy number value for the three combined amy1 regions, amy2a […]

2013
PMCID: 3689680
PMID: 23805272
DOI: 10.1371/journal.pone.0066729

[…] were mapped to the human reference genome, which was masked by repeatmasker and trf programs, using mrfast (v2.0.0.5) and allowing up to 5% mismatches. then, copy number over 5 kb was predicted by mrcanavar (v0.3)., snp genotyping and cnv detection were performed using the illumina infinium hd assay system (humanomni2.5-quad). genomic dna from the twins were tested on duplicated arrays. data […]

mrCaNaVaR institution(s)
Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA

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