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Bis-SNP specifications


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


No version available


  • person_outline Benjamin P. Berman

Publication for Bis-SNP

Bis-SNP citations


Global misregulation of genes largely uncoupled to DNA methylome epimutations characterizes a congenital overgrowth syndrome

Sci Rep
PMCID: 5627257
PMID: 28978943
DOI: 10.1038/s41598-017-13012-z

[…] ters. Only uniquely aligned reads were used for subsequent analyses. In order to distinguish the C > T SNPs from C > T substitutions that were caused by sodium bisulfite conversion in the F1 fetuses, Bis-SNP (version: 0.82.2) was used to perform the SNP calling. Only CpG sites that showed consensus CpG context for both parental alleles (i.e., do not overlap any SNPs identified by Bis-SNP) were use […]


De novo DNA methylation during monkey pre implantation embryogenesis

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

[…] 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 ident […]


Nucleosome Positioning and NDR Structure at RNA Polymerase III Promoters

Sci Rep
PMCID: 5296907
PMID: 28176797
DOI: 10.1038/srep41947

[…] ation. 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 (; all data used in this study is past the 9-months m […]


Epigenetic regulation of lateralized fetal spinal gene expression underlies hemispheric asymmetries

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

[…] -to-A 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 read […]


reChIP seq reveals widespread bivalency of H3K4me3 and H3K27me3 in CD4+ memory T cells

Nat Commun
PMCID: 4992058
PMID: 27530917
DOI: 10.1038/ncomms12514

[…] 40.1 × 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. […]


Epigenetic dynamics of monocyte to macrophage differentiation

PMCID: 4967341
PMID: 27478504
DOI: 10.1186/s13072-016-0079-z

[…] adapter trimmed (Trim Galore!), mapped using bwa [] to the human reference genome (hs37d5) followed by removal of duplicate reads. Methylation levels of CpGs and GpCs, respectively, were called using Bis-SNP []. Cytosines in a GCG context were excluded from further analysis. Bisulfite conversion efficiency was checked genome wide with all cytosines in an HCH context.NOMe-seq peaks were called with […]


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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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