SOAPsnp pipeline

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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Publication for SOAPsnp

SOAPsnp citations

 (7)
2017
PMCID: 5589652

[…] region and sequencing depth computation, snp and indel calling, and cnv detection. first, a novel three-step computational frame work for cnv was applied. then, snps and indels were called using soapsnp software and sam tools pileup software, respectively. a snp or indel would be filtered out if it could not follow the criterion: supported by at least 10 reads and > 20% of the total […]

2017
PMCID: 5687609

[…] region and sequencing depth computation, snp and indel calling, and cnv detection. first, a novel three-step computational frame work for cnv was applied. then, snps and indels were called using soapsnp software and sam tools pileup software, respectively. a snp or indel was be filtered if it could not follow the criterion: supported by at least 10 reads and >20% of the total reads. […]

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 […]

2014
PMCID: 3943834

[…] and the coverage of the target region for each screened sample are provided in figure  1., the target region capture performance is presented in average value of all 76 the sequenced samples., using soapsnp and samtools for variant calling [21,22], we obtained a total of 15875 variants in the 117 genes on average pr. sample, including 13808 snps and 2067 indels. all variants were annotated […]

2014
PMCID: 4004585

[…] on either an illuminahiseq 2000 or solid platform. sequence data were mapped using bwa (burrows-wheeler aligner) against hg18 (ncbi36) human genome as a reference. variants were called using soapsnp and soapindel (from the short oligonucleotide analysis package) with medium stringency (supplementary table 1)., primers were designed to amplify the coding exons of ifih1 (supplementary […]

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

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