avalind/msmut_notes.md

## msmut_notes.md

      
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              msmut_notes.md
            
          
    MSMutect notes

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.
on line 211 in Python_managing_file.py vec[:,fi[0]] would sometimes (also on the Normal.bam test data) raise an IndexError,
when wrapping this in a try-catch clause the shell_for_all.sh would run without problems for the Normal.bam and Tumor.bam and ms_indel_calling.sh would also run without problems but the resulting maf_like-files would be all empty.

Internal UPPMAX notes

To setup a fitting environment on the milou cluster;
module load bioinfo-tools BEDTools/2.26.0 R/2.15.2 java/sun_jdk1.8.0_92 bowtie2/2.3.2 gcc/4.8 python/2.7