SOAPsnp specifications

Information


Unique identifier OMICS_00078
Name SOAPsnp
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

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SOAPsnp article

SOAPsnp citations

 (7)
2016
PMCID: 4906935

[…] sequences. sequences were compared with burrows wheeler aligner (bwa; multi-vision software package; version 0.7.12-r1039) and hg19 software (1). concurrently, sequence capture was evaluated using soapsnp (version 1.03), saopindel (version 2.01) and samtools software (version 0.1.18) (2,3). initially, single nucleotide variants, insertion sand deletions were excluded using information […]

2016
PMCID: 4991830

[…] in the reference and unmapped reads. average sequencing depth and coverage were calculated using the alignment results.20 the mapped reads were then used to detect snps, indels, and svs using soapsnp and soapsv software with default parameter settings.20–22 the snps identified were filtered based on the following stringent criteria: no less than two times for coverage depth (no less […]

2015
PMCID: 4613280

[…] reads” derived from targeted sequencing and filtering were then aligned to the human reference genome (hg19/grch37) using the bwa (burrows wheeler aligner) multi-vision software package. we used soapsnp software and samtools to detect single nucleotide variants and indels [21]., sanger sequencing was used to determine whether any of the variants co-segregated with the disease phenotype […]

2015
PMCID: 4534381

[…] map all of the m. notabilis genome reads from 12 libraries [38] onto the reference sequence, a 3709-bp fragment located at scaffold2247 (genbank accession number kf784877). snps were detected using soapsnp essentially as described [37], but with the following modifications: soapsnp calls were discarded if the quality score of the consensus genotype was less than 20, if the sequencing depth […]

2014
PMCID: 4020765

[…] using soapaligner [21]. after that, the duplicated reads were filtered out and the clean reads located in the target region were collected. the consensus of genotype and quality were estimated by soapsnp (version1.03) using the clean reads. the variations of low quality were filtered out according to the following criteria: (i) quality score <20 (q20); (ii) average copy number […]

SOAPsnp institution(s)
Beijing Genomics Institute at Shenzhen, Shenzhen, China

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