Step 2 - Improper reads onwards, bwa-mem fails to read index files

[hevmarriott]

Hi there,

From the improper reads step, bwa-mem fails to read the index files - I did index both the input bam and reference genome fa files, which is why the previous step 'Chimeric and split reads' worked. Beyond that, bwa-mem does not want to work.

Any help would be much appreciated!