SOAPsnp protocols

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SOAPsnp computational protocol

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 IN pipelines

 (25)
2018
PMCID: 5894961
PMID: 29641573
DOI: 10.1371/journal.pone.0185237

[…] table 2. the reference was obtained from the ncbi, version grch37 (hg19). sequence alignment was performed using burrows wheeler aligner (bwa) multi-vision software package [13]. snvs were called by soapsnp [14] 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 […]

2017
PMCID: 5243127
PMID: 28099493
DOI: 10.1371/journal.pone.0170011

[…] soapaligner program was then used to align the read sequences to the human reference genome (hg19). after duplicates had been removed using picard software, the snps and indels were identified using soapsnp and gatk programs. subsequently, the reads were realigned to the reference genome using bwa. the identified snps and indels were annotated using the exome-assistant program. magicviewer […]

2017
PMCID: 5341019
PMID: 28272483
DOI: 10.1038/srep43939

[…] command bwa-mem)28. sequence alignment/map (sam) format alignment result files were imported to samtools29 and the ‘rmdup’ command was used to remove potential pcr duplicates. snps were detected by soapsnp8 and annotated with annovar30. snps with minor allele frequencies (maf) less than 0.05 and deviated from hardy-weinberg equilibrium (p < 0.001) were excluded. haploview21 was used […]

2017
PMCID: 5518093
PMID: 28724398
DOI: 10.1186/s12881-017-0418-3

[…] only two de novo cnvs were identified in the proband. however, both cnvs were reported as polymorphisms in the database of genomic variants (dgv)., single nucleotide variants (snvs) were detected by soapsnp (v.1.05). indels were identified by gatk. annovar was used to annotate the variants. the number of variants among samples ranged from 6,288,378 to 6,375,627 (fig. 2a, additional file 2: table […]

2016
PMCID: 4716855
PMID: 26819646
DOI: 10.7150/jca.13150

[…] using an illumina hiseq instrument. average fragment size used for sequencing was about 480 bp. each library was subjected to 2 lanes, resulting in at least 60-fold haploid coverage for each sample. soapsnp 29 was used to detect single nucleotide polymorphisms (snps); samtools 30 was used to detect the indels (small insertion/deletion); crest 31 was used to detect structure variations (svs, […]

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

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