You should change the directory where it says
/path/to/bams/ to wherever you have stored your alignment files. Note that delly can work from bam or cram format, so no need to convert. This command should product a new bcf file for each sample (ending in .genotyped.bcf). We will now merge the genotyped bcfs. Since the files all contains calls for the same deletions (with specific IDs assigned during the previous
delly merge step), this time the merge command will be slightly different. The resulting file will not only contain the positions, but also the calls for each sample.