Coval protocols

Coval specifications


Unique identifier OMICS_14832
Name Coval
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input data SAM/BAM alignment data
Output data The called SNPs/indels.
Biological technology Illumina
Operating system Unix/Linux
Programming languages Perl
Computer skills Advanced
Version 1.5
Stability Stable
Maintained Yes



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  • person_outline Shunichi Kosugi <>

Publication for Coval

Coval IN pipeline

PMCID: 3707850
PMID: 23874658
DOI: 10.1371/journal.pone.0068529

[…] (ddbj sequence read archive: dra000927) using bwa (burrows-wheeler aligner) software [21]. alignment files were converted to sam/bam files using samtools [22], and applied to the snp-calling filter “coval” we previously developed (kosugi et al. unpublished data; abe et al. [7]) to increase snp-calling accuracy. following snp-index calculation for all snp positions, we excluded snps […]

Coval institution(s)
Iwate Biotechnology Research Center, Kitakami, Iwate, Japan; Kazusa DNA Research Institute, Kisarazu, Chiba, Japan; The Sainsbury Laboratory, Norwich Research Park, Norwich, UK
Coval funding source(s)
This work was supported by the Program for Promotion of Basic Research Activities for Innovative Biosciences (PROBRAIN), the Ministry of Agriculture, Forestry, and Fisheries of Japan and Grant-in-aid for Scientific Research from the Ministry of Education, Cultures, Sports and Technology, Japan (Grant-in-Aid for Scientific Research on Innovative Areas 23113009) and by JSPS KAKENHI Grant Number 22510217; and by the Gatsby Charitable Foundation.

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