I finally got it working. Thanks to the hint that the whitespace might be the problem, I found this HOW-TO. The solution is the eval command.
Code:
... command="$stampy -g $ref_genome -h $ref_genome -o $out --bwa=$bwa --bwaoptions=\"$q10 $bwa_ref\" -M $seq1 $seq2" eval $command
Leave a comment: