Analysing multiple bam files simultaneously

[sgrannem]

The documentation suggests that multiple bam files can be analysed by the pipeline, however, this did not work for me. I was only able to run one bam file at a time.

-b /bam_files/*.bam

This did not work. It says that it doesn't understand the command line arguments and then prints out the list of filenames.

-b /bam_files/myfirstdataset.bam did work fine.

So I had to run a for loop in bash to analyse all my datasets.

[janoppelt]

The manual says:
-b B the full path one or many bam/sam files (many files should be provided with a pattern, **within double quotes**: e.g. **"your_bam_folder/*.bam"**)

Try to change your command to:
-b "/bam_files/*.bam" (notice the "")