modules/gatk_unifiedgenotyper

Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]

Sorted and indexed BAM/CRAM/SAM file

BAM index file

Groovy Map containing reference information.
e.g. [ id:'test', single_end:false ]

Reference file used to generate BAM file

Groovy Map containing reference information.
e.g. [ id:'test', single_end:false ]

Index of reference file used to generate BAM file

Groovy Map containing reference information.
e.g. [ id:'test', single_end:false ]

GATK dict file for reference

Groovy Map containing reference information.
e.g. [ id:'test', single_end:false ]

Bed file with the genomic regions included in the library (optional)

Groovy Map containing file meta-information for the contamination file.
e.g. [ id:'test', single_end:false ]

Tab-separated file containing fraction of contamination in sequencing data (per sample) to aggressively remove

Groovy Map containing file meta-information for the dbsnps file.
e.g. [ id:'test', single_end:false ]

VCF file containing known sites (optional)

Groovy Map containing file meta-information for the VCF comparison file.
e.g. [ id:'test', single_end:false ]

Comparison VCF file (optional)