Identify chromosomal rearrangements.
meta
Groovy Map containing sample information e.g. [ id:‘test’, single_end
input
BAM/CRAM file
*.{bam,cram}
input_index
BAM/CRAM index file
*.{bai,crai}
meta2
Groovy Map containing sample information e.g. [ id:'test_fasta']
[ id:'test_fasta']
fasta
Input FASTA file
*.{fasta,fa}
meta3
Groovy Map containing sample information from bwa index e.g. [ id:'test_bwa-index' ]
[ id:'test_bwa-index' ]
bwa_index
BWA genome index files
Directory containing BWA index *.{amb,ann,bwt,pac,sa}
vcf
*.{vcf}
ploidy
tab
*.{ploidies.tab}
versions
File containing software versions
versions.yml
Search for structural variants.
