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Protocols

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

 (295)
library_books

Whole Exome Sequencing Identified a Novel Heterozygous Mutation in HMBS Gene in a Chinese Patient With Acute Intermittent Porphyria With Rare Type of Mild Anemia

2018
PMCID: 5920022
PMID: 29731767
DOI: 10.3389/fgene.2018.00129

[…] reference genome (hg19) with maximum 3 mismatches, the parameters were set as ‘-a -b -d -o -u -2 -t -v 3 -l 35 -s 40 -m 0 -x 500 -p 4 -r 1 -n 0’. based on the results from soapaligner, software soapsnp (v1.05) was used to assemble the consensus sequence and call genotypes in target regions. the following parameters were set: -q k -i -d -o -r 0.0005 -e 0.001 -u -l 90 -t -s -2,where ‘-t’ used […]

call_split

Systematic evaluation of a targeted gene capture sequencing panel for molecular diagnosis of retinitis pigmentosa

2018
PMCID: 5894961
PMID: 29641573
DOI: 10.1371/journal.pone.0185237
call_split See protocol

[…] in . the reference was obtained from the ncbi, version grch37 (hg19). sequence alignment was performed using burrows wheeler aligner (bwa) multi-vision software package []. snvs were called by soapsnp [] and small indels (<20bp) were identified using the samtools (tools for alignments in the sam format) version: 0.1.18, http://samtools.sourceforge.net/., the screening method of copy […]

library_books

Intraspecific comparative genomics of isolates of the Norway spruce pathogen (Heterobasidion parviporum) and identification of its potential virulence factors

2018
PMCID: 5870257
PMID: 29580224
DOI: 10.1186/s12864-018-4610-4

[…] least 1000 bp. the resulting subreads were self-corrected by falcon genome assembly tool kit v.0.3.0 and assembled into contigs by celera assembler v.8.3 [] followed by single base corrections using soapsnp v.1.05 [] and soapindel v.1.08 [] pipelines with hiseq pe reads. scaffolding was performed by sspace- longread [] using hiseq mp reads., filtered reads of re-sequenced isolates were assembled […]

library_books

Genetic analysis of sick sinus syndrome in a family harboring compound CACNA1C and TTN mutations

2018
PMCID: 5928663
PMID: 29568937
DOI: 10.3892/mmr.2018.8773

[…] reads, the adapter sequence was removed and the purification data analyzed by sequence alignment. soap software (soapdenovo v2.04; soap3/gpu v0.01beta; soapaligner/soap2 v2.20; soapsplice v1.1; soapsnp v1.03; soapindel v1.0; soapsv v1.02) was used to analyze copy number, single nucleotide polymorphism (snp), and insertion/deletion (indel). annotations were used to screen suspected […]

library_books

A unique homozygous WRAP53 Arg298Trp mutation underlies dyskeratosis congenita in a Chinese Han family

2018
PMCID: 5842585
PMID: 29514627
DOI: 10.1186/s12881-018-0549-1

[…] was used for library preparation, and a nimblegen sequence capture array was used for sequence capture. illumina pipeline software (version 1.3.4) was used to analyze the primary sequencing data. soapsnp software and sam tools pileup software were used to analyze the gene mutations., to confirm the wrap53 arg298trp mutation identified by ngs, the corresponding wrap53 gene region surrounding […]

library_books

Phenotypic and genotypic characterization of inflammatory bowel disease in children under six years of age in China

2018
PMCID: 5840468
PMID: 29531467
DOI: 10.3748/wjg.v24.i9.1035

[…] 3′-/5′- adapters and low-quality reads, respectively. clean short reads were mapped to the human genome (hg19) using burrows wheeler aligner software (http://sourceforge.net/projects/bio-bwa/). soapsnp software (http: //soap.genomics.org.cn/) and sam tools pileup software (http://sourceforge.net/projects/samtools/) were used to detect single-nucleotide polymorphisms and small insertions […]


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

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