SNPsplit is an allele-specific alignment sorter which is designed to read in alignment files in SAM/BAM format and determine the allelic origin of reads that cover known SNP positions.
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Krueger F, Andrews SR.
SNPsplit: Allele-specific splitting of alignments between genomes with known SNP genotypes.
F1000Res. 2016 Jun 23;5:1479. doi: 10.12688/f1000research.9037.2. PMID: 27429743; PMCID: PMC4934512.