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SNPsplit specifications


Unique identifier OMICS_14190
Name SNPsplit
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format BAM, SAM
Operating system Unix/Linux
Programming languages Perl
License GNU General Public License version 3.0
Computer skills Advanced
Version 0.3.1
Stability Stable
Maintained Yes




No version available



Publication for SNPsplit

SNPsplit citations


hnRNPK Recruits PCGF3/5 PRC1 to the Xist RNA B Repeat to Establish Polycomb Mediated Chromosomal Silencing

Mol Cell
PMCID: 5735038
PMID: 29220657
DOI: 10.1016/j.molcel.2017.11.013

[…] the parameters ‘–outfiltermultimapnmax 1 –outfiltermismatchnmax 2 –alignendstype endtoend’ for all the 4su-seq libraries (). unique alignments were retained for further analysis. we employed the snpsplit to separate the alignment into distinct alleles (cast and 129s1) with the paired mode. the summary of the allelic split is listed in . to call the allelic gene expression, the number […]


Contribution of epigenetic landscapes and transcription factors to X chromosome reactivation in the inner cell mass

Nat Commun
PMCID: 5670228
PMID: 29101321
DOI: 10.1038/s41467-017-01415-5

[…] our data, using the same parameters, parental genomes, annotations and snps files. briefly, we have filtered the single-nucleotide polymorphisms (snps) on their quality values (f1 values), thanks to snpsplit tool (v0.3.0). a snp on chr:x 37,805,131 (mm10) in rhox5 gene, annotated a for c57bl/6j and g for all other strains (included c57bl/6nj) was discarded because it was missing in our samples. […]


Comprehensive Cell Surface Protein Profiling Identifies Specific Markers of Human Naive and Primed Pluripotent States

Cell Stem Cell
PMCID: 5459756
PMID: 28343983
DOI: 10.1016/j.stem.2017.02.014

[…] reads were trimmed using trim galore v0.4.2 and aligned to the n-masked genome using hisat2 (default settings but without soft-clipping). the mapped data was sorted into allele-specific reads using snpsplit (v0.3.1, default parameters, single-end) (). genome1/genome2 reads, which corresponded to reads carrying either of the two snps, were imported into seqmonk. probes were designed […]


Clonally stable Vκ allelic choice instructs Igκ repertoire

Nat Commun
PMCID: 5459994
PMID: 28555639
DOI: 10.1038/ncomms15575

[…] using bowtie2 (ref. ), after masking nucleotides located on snps from the cast genome (sanger mouse genome project—release 1505). reads falling on snps were then sorted to genome of origin using snpsplit (babraham institute) and pcr duplicates removed using picard (broad institute). read coverage tracks were made using bedtools. read pairs were assigned to a specific vκ segment […]


Setdb1 mediated H3K9 methylation is enriched on the inactive X and plays a role in its epigenetic silencing

PMCID: 4870784
PMID: 27195021
DOI: 10.1186/s13072-016-0064-6

[…] before the 7 5’ most bases and 8 3’ most bases were trimmed based on m-bias [] results produced by bismark. reads were then split into either mus musculus castaneus or mus musculusdomesticus using snpsplit ( where c/t snps are excluded to eliminate errors due to the bisulphite conversion. methylation calls were made using the bismark […]

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SNPsplit institution(s)
Bioinformatics Group, The Babraham Institute, Cambridge, UK
SNPsplit funding source(s)
Supported by the Babraham Institute and the UK Biotechnology and Biological Sciences Research Council (BBSRC).

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