bam_variant_calling_sort_freebayes_bcftools

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

BAM/CRAM/SAM file;

Index BAI/CRAI/CSI file

BAM/CRAM/SAM file; used to run variant calling with pair (normal vs tumor)

Index BAI/CRAI/CSI file

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

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

reference fasta file

reference fasta file index

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

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

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