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SOAPsnp specifications


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


No version available

Publication for SOAPsnp

SOAPsnp citations


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

Front Genet
PMCID: 5920022
PMID: 29731767
DOI: 10.3389/fgene.2018.00129
call_split See protocol

[…] human 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 […]


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

BMC Genomics
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 de […]


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

BMC Med Genet
PMCID: 5842585
PMID: 29514627
DOI: 10.1186/s12881-018-0549-1
call_split See protocol

[…] kit 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. […]


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

PMCID: 5840468
PMID: 29531467
DOI: 10.3748/wjg.v24.i9.1035
call_split See protocol

[…] emove 3′-/5′- adapters and low-quality reads, respectively. Clean short reads were mapped to the human genome (hg19) using Burrows Wheeler Aligner software ( SOAPsnp software (http: // and SAM tools Pileup software ( were used to detect single-nucleotide polymorphisms and small insertions and […]


Mutation of IFNLR1, an interferon lambda receptor 1, is associated with autosomal dominant non syndromic hearing loss

J Med Genet
PMCID: 5931241
PMID: 29453195
DOI: 10.1136/jmedgenet-2017-104954

[…] out low-quality and duplicate reads, clean data were aligned to the human reference genome hg19 using the Burrows-Wheeler Aligner. After alignment, variants were called using four types of software (SOAPsnp, GATK, Samtools and Platypus), merged into variant call format files and annotated using a variant effect predictor, including those with minor allele frequencies (MAF), in public databases an […]


Transcription Associated Mutation Promotes RNA Complexity in Highly Expressed Genes—A Major New Source of Selectable Variation

Mol Biol Evol
PMCID: 5913671
PMID: 29420738
DOI: 10.1093/molbev/msy017

[…] b) of clean RNA-seq data for each falcon and 5.0 Gb for each chicken (, online). Reads from each individual were aligned to the reference genome () using SOAP v2.21 (), followed by SNP calling using SOAPsnp v1.04 (), yielding 377,530 SNPs after filtering (, online). To obtain the highest quality data set, only those sites covered by reads in all individuals were analyzed. The final data set comp […]


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

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