modules/freebayes

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

BAM/CRAM/SAM file

BAM/CRAM/SAM index file

BAM/CRAM/SAM file

BAM/CRAM/SAM index file

Optional - Limit analysis to targets listed in this BED-format FILE.

Groovy Map containing reference information.
e.g. [ id:‘test_reference’ ]

reference fasta file

Groovy Map containing reference information.
e.g. [ id:‘test_reference’ ]

reference fasta file index

Groovy Map containing meta information for the samples file.
e.g. [ id:‘test_samples’ ]

Optional - Limit analysis to samples listed (one per line) in the FILE.

Groovy Map containing meta information for the populations file.
e.g. [ id:‘test_populations’ ]

Optional - Each line of FILE should list a sample and a population which it is part of.

Groovy Map containing meta information for the cnv file.
e.g. [ id:‘test_cnv’ ]

A copy number map BED file, which has either a sample-level ploidy:
sample_name copy_number
or a region-specific format:
seq_name start end sample_name copy_number