The cluster_identifier tool of Scramble identifies soft clipped clusters
meta
Groovy Map containing sample information e.g. [ id:‘test’, single_end
input
BAM/CRAM file
*.{bam,cram}
input_index
Index of the BAM/CRAM file
*.{bai,crai}
fasta
The reference FASTA file (mandatory when using CRAM files)
*.{fasta,fa}
versions
File containing software versions
versions.yml
clusters
Tab-delimited file containing the soft-clipped clusters
*.clusters.txt
Soft Clipped Read Alignment Mapper
