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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




No version available


  • person_outline Shunichi Kosugi

Publication for Coval

Coval citations


Genome sequencing of the staple food crop white Guinea yam enables the development of a molecular marker for sex determination

BMC Biol
PMCID: 5604175
PMID: 28927400
DOI: 10.1186/s12915-017-0419-x

[…] ifying P4- and P3-specific heterozygous positions, the Illumina reads from the two bulk-sequenced samples (male and female bulks) were aligned to the reference sequences using BWA [] and subjected to Coval filtering [] as previously described. When the P3 reference sequence was used for alignment, the SNP-index values were calculated only at all of the P4-specific heterozygous positions. By contra […]


Exome QTL seq maps monogenic locus and QTLs in barley

BMC Genomics
PMCID: 5288901
PMID: 28148242
DOI: 10.1186/s12864-017-3511-2
call_split See protocol

[…] s were detected, and the average values were calculated by sliding window analysis. The “window size” was configured from 100 kbp to 1 Mbp, and “slide size” was set to 10 kbp. The SNP-calling filter “Coval” [] was set to 6. Next, SNP positions with a SNP index of <0.3 were excluded, and a threshold of more than seven mismatches and a depth of fewer than four were eliminated, as these SNPs may be d […]


Development and utilization of a new chemically‐induced soybean library with a high mutation density†

PMCID: 5248594
PMID: 27774740
DOI: 10.1111/jipb.12505
call_split See protocol

[…] ED quality (Q) score <20. After data pre‐processing, clean reads were aligned to the Williams 82 reference sequence using BWA (Li and Durbin ) software, and the aligned short reads were filtered with Coval to improve SNP calling accuracy. SNP identification was performed using the Genome Analysis Toolkit (GATK, McKenna et al. ) and SAMtools (Li et al. ). A detailed description of the protocol we u […]


QTL‐seq for rapid identification of candidate genes for 100‐seed weight and root/total plant dry weight ratio under rainfed conditions in chickpea

Plant Biotechnol J
PMCID: 5095801
PMID: 27107184
DOI: 10.1111/pbi.12567

[…] calculating SNP‐index. Briefly, the cleaned reads of donor parent (ICC 4958) were first aligned to the reference genome (CDC Frontier; Varshney et al., ) using inbuilt BWA aligner (Li and Durbin, ). Coval was used for postprocessing and filtering of the alignment files (Kosugi et al., ). The variants called were then used to develop reference‐based assembly of the donor parent (ICC 4958) by subst […]


Host specialization of the blast fungus Magnaporthe oryzae is associated with dynamic gain and loss of genes linked to transposable elements

BMC Genomics
PMCID: 4870811
PMID: 27194050
DOI: 10.1186/s12864-016-2690-6

[…] AMtools. We regarded positions where no short reads were aligned as unknown nucleotides. When nucleotides were different from those of the reference genome but were not regarded as homozygous SNPs by Coval, we also treated them as unknown nucleotides. Synonymous divergence (dS) and nonsynonymous divergence (dN), and omega (dN/dS) between M. oryzae and M. grisea isolates were estimated based on the […]


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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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