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SNPsplit website  

SNPsplit is an allele-specific alignment sorter which is designed to read alignment files in SAM/ BAM format and determine the allelic origin of reads that cover known SNP positions.

Environment Modules

Run module spider SNPsplit to find out what environment modules are available for this application.

System Variables

  • HPC_SNPSPLIT_DIR - installation directory
  • HPC_SNPSPLIT_BIN - executable directory


If you publish research that uses SNPsplit you have to cite it as follows:

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