Bis-SNP protocols

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Bis-SNP specifications

Information


Unique identifier OMICS_00591
Name Bis-SNP
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format BAM
Output format Tab-delimited text, VCF
Operating system Unix/Linux
Programming languages Java, Perl
License MIT License
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


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Maintainer


  • person_outline Benjamin P. Berman <>

Publication for Bis-SNP

Bis-SNP in pipeline

2014
PMCID: 4203885
PMID: 25239471
DOI: 10.1186/s13059-014-0469-0

[…] hscs v.1.5.15.1. image analysis and base calling were carried out using rta 1.13.48.0, and deconvolution and fastq file generation were carried out using casava_v1.7.1a5. raw reads were mapped using bis-snp [], and percentage methyl-c/c was calculated for every cpg dinucleotide in the human genome. all cpg dinucleotides with a minimum sequencing coverage of 3× were used for downstream analyses. […]


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Bis-SNP in publications

 (16)
PMCID: 5627257
PMID: 28978943
DOI: 10.1038/s41598-017-13012-z

[…] the parental origins of the alleles in the b. t. indicus × b. t. taurus f1 progenies, we obtained heterozygous snps of the fetuses from two sources: 1) snps identified from the wgbs data using bis-snp and 2) snps identified from the rnaseq data of the f1 hybrids (supplementary fig. ). we assigned the wgbs reads overlapping the snps to their parental origins based on the genotype of the b. […]

PMCID: 5385613
PMID: 28233770
DOI: 10.1038/cr.2017.25

[…] remain hypomethylated ()., to address whether both paternal and maternal genomes similarly undergo active dna demethylation or whether only one parental genome goes through this process, we applied bis-snp algorithm (see materials and methods) to call single-nucleotide polymorphisms (snps) to track paternal and maternal genomes. we obtained 5 070 snps whose parental origin could be clearly […]

PMCID: 5296907
PMID: 28176797
DOI: 10.1038/srep41947

[…] the bisulfite inconversion rate was 0.9%. nome-seq sequencing reads were aligned to the hg19 genome using bsmap (xi 2009). methylation levels of cpg and gpc dinucleotides were determined using bis-snp and previously described parameters. chip-seq data for pol iii and pol ii peaks were downloaded from encode (http://genome.ucsc.edu/encode/); all data used in this study is past the 9-months […]

PMCID: 5295814
PMID: 28145864
DOI: 10.7554/eLife.22784.013

[…] version, bismark (rrid:scr_005604) () and bowtie2 () were applied on the sequence reads in order to align them to the in silico converted reference (homo sapiens, hg19), which was refined using bis-snp (rrid:scr_005439) () adopted gatk (rrid:scr_001876) (; ) modules. bis-snp then simultaneously determined the genotypes and methylation rates at each cpg site using bayesian inference. dna […]

PMCID: 4992058
PMID: 27530917
DOI: 10.1038/ncomms12514

[…] × coverage) of which 1,508,942,939 (93.67%) were mapped using bwa. for the bisulfite conversion efficiency, we calculated 99.92% using all hch-positions and methylation calls were generated with bis-snp., paired-end reads from sequencing chromatin input, primary chip and rechip libraries were mapped to the human genome version hs37d5 with cnybwa version 0.6.2, which is a hardware […]


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Bis-SNP institution(s)
USC Epigenome Center, University of Southern California, Los Angeles, CA, USA; Genetics, Molecular and Cellular Biology Program, University of Southern California, Los Angeles, CA, USA; Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA

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