Bisulfilter

Tool for filtering BSSeeker2 [1] methylation calls obtained by whole genome bisulfite sequencing.

More specifically, this Python3 tool filters CGmap files generated by BSSeeker2 according to criteria specified by the user. Alternatively, it can also summarize the CG map file based on these criteria

If you use this tool, please cite: B Cuypers, F Dumetz, P Meysman, K Laukens, G De Muylder, J-C Dujardin, MA Domagalska The absence of C-5 DNA methylation in Leishmania donovani allows DNA enrichment from complex samples

Usage: python Bisulfilter.py [-h] [-s] [-c INT] [-m FLOAT] CGmap

positional arguments:
  CGmap       input CGmap

optional arguments:
  -h, --help  show this help message and exit
  -s          show summary instead
  -c INT      minimal number of reads covering the postion for it to be
              reported (default: 25)
  -m FLOAT    proportion of reads that need to be methylated for a specific
              position for it to be reported (default: 0.8)

For all questions, problems and suggestions please contact the author Bart Cuypers at bart.cuypers@uantwerpen.be

[1] 1. Guo W, Fiziev P, Yan W, Cokus S, Sun X, Zhang MQ, Chen P-Y, Pellegrini M: BS-Seeker2: a versatile aligning pipeline for bisulfite sequencing data. BMC genomics 2013, 14(1):774.