Entering edit mode
3.5 years ago
storm1907
▴
30
Hello, when trying to run Lofreq tool for low frequency variant calling with mpileup files, the tool is looking for header in the input (but there should not be one) when running Lofreq with binary files, tool does not work either Here https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3526318/ it is said, that piled files are used for input, but in Github I see that people run Lofreq with bam files Which Lofreq input type is correct? Or maybe I should add header to mpileup files somehow manually?
Have you checked the documentation where it describes the necessary inputs?