Format

Send to

Choose Destination
Version 2. F1000Res. 2016 Jun 23 [revised 2016 Jul 27];5:1479. doi: 10.12688/f1000research.9037.2. eCollection 2016.

SNPsplit: Allele-specific splitting of alignments between genomes with known SNP genotypes.

Author information

1
Bioinformatics Group, The Babraham Institute, Cambridge, UK.

Abstract

Sequencing reads overlapping polymorphic sites in diploid mammalian genomes may be assigned to one allele or the other. This holds the potential to detect gene expression, chromatin modifications, DNA methylation or nuclear interactions in an allele-specific fashion. SNPsplit is an allele-specific alignment sorter designed to read files in SAM/BAM format and determine the allelic origin of reads or read-pairs that cover known single nucleotide polymorphic (SNP) positions. For this to work libraries must have been aligned to a genome in which all known SNP positions were masked with the ambiguity base 'N' and aligned using a suitable mapping program such as Bowtie2, TopHat, STAR, HISAT2, HiCUP or Bismark. SNPsplit also provides an automated solution to generate N-masked reference genomes for hybrid mouse strains based on the variant call information provided by the Mouse Genomes Project. The unique ability of SNPsplit to work with various different kinds of sequencing data including RNA-Seq, ChIP-Seq, Bisulfite-Seq or Hi-C opens new avenues for the integrative exploration of allele-specific data.

KEYWORDS:

ASB; ASE; ASM; Allele; Allele-specific; N-masking; SNP

Supplemental Content

Full text links

Icon for F1000 Research Ltd Icon for PubMed Central
Loading ...
Support Center