SNPsplit

Allele-specific alignment sorter. Determines allelic origin of reads that cover known SNP positions

https://www.bioinformatics.babraham.ac.uk/projects/SNPsplit/

Currently only the "Allele-tagging" and "Allele-sorting" reports are supported.

The log files from the genome creation steps are not parsed and there are no plots/tables produced from the "SNP coverage" report.

Differences between the numbers in the tagging and sorting reports are due to paired-end reads. For these, if only a single mate in a pair is assigned to a genome then it will "rescue" its mate and both will be "sorted" into that genome (even though only one of them was tagged). Conversely, if the mates in a pair are tagged as arising from different genomes, then the pair as a whole is unassignable.

File search patterns

snpsplit/new:
  fn: "*SNPsplit_report.yaml"
snpsplit/old:
  contents: "Writing allele-flagged output file to:"
  num_lines: 2