The cluster_identifier tool of Scramble identifies soft clipped clusters
meta
:map
Groovy Map containing sample information e.g. [ id:‘test’ ]
input
:file
BAM/CRAM file
*.{bam,cram}
input_index
Index of the BAM/CRAM file
*.{bai,crai}
meta2
Groovy Map containing information about the fasta file e.g. [ id:‘test’ ]
fasta
The reference FASTA file (mandatory when using CRAM files)
*.{fasta,fa}
clusters
*.clusters.txt
Tab-delimited file containing the soft-clipped clusters
versions
versions.yml
File containing software versions
Soft Clipped Read Alignment Mapper
