I've run in to the following issues while trying to get MSMutect to work:
- the path to the data folder in shell_for_all.sh needs to be absolute.
- make a symlink with link name phobos in bin, pointing to the correct phobos binary.
- bowtie2 needs to have its indices specified by the -x flag, so this needs to be added to the awk-oneliner invoking bowtie2 for each repeat.
- Even when adding the -x flag bowtie2 complains about some missing reference files (using the Normal.bam) test data.