SNPsplit protocols

View SNPsplit computational protocol

SNPsplit statistics

To access cutting-edge analytics on consensus tools, life science contexts and associated fields, you will need to subscribe to our premium service.

Subscribe
info

Citations per year

Citations chart
info

Popular tool citations

chevron_left Genome assembly chevron_right
Popular tools chart
info

Tool usage distribution map

Tool usage distribution map
info

Associated diseases

Associated diseases

SNPsplit specifications

Information


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

Download


Versioning


Add your version

Documentation


Maintainer


Publication for SNPsplit

SNPsplit in pipelines

 (2)
2017
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 […]

2017
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 […]


To access a full list of citations, you will need to upgrade to our premium service.

SNPsplit in publications

 (5)
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 […]

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. […]

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 […]

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 […]

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 (www.bioinformatics.babraham.ac.uk/projects/snpsplit/) where c/t snps are excluded to eliminate errors due to the bisulphite conversion. methylation calls were made using the bismark […]


To access a full list of publications, you will need to upgrade to our premium service.

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).

SNPsplit reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review SNPsplit