samtools sort command is enough to create right input for meth.call. Could you be a bit more specific about the error message your are receiving or issues with meth.call?
Thank you for your quick reply. See my error message below:
Extracting methylation information from input SAM files and creating output files for each sample...
sam_type not specified
Error in FUN(X[[i]], ...) :
Error in methylation calling...
Check if it is a sorted Bismark SAM file
You need to convert sorted bam to sam to be able to input into methylPipe. I am unable to regenerate the error message you receive on any of my files. Could you send me a subset of the sam error file (say first 100000 reads)?
One of the user sorted this error because instead of the input folder, he was specifying an individual file.sam, resulting in this error message. Please make sure to provide the correct parameters as mentioned in documentation. If someone still face same error then let me know.