SNPsplit pipeline

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
Requirements SAMtools
Maintained Yes



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  • person_outline Felix Krueger <>

Publication for SNPsplit

SNPsplit IN pipelines

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) (krueger and andrews, 2016). genome1/genome2 reads, which corresponded to reads carrying either of the two snps, were imported into seqmonk. probes […]

PMCID: 5459994
PMID: 28555639
DOI: 10.1038/ncomms15575

[…] using bowtie2 (ref. 37), 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 snpsplit39 (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 […]

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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