Tools for population-scale genotyping using pangenome graphs.
Input
Name (Type)
Description
Pattern
meta (map)
Groovy Map containing sample information
e.g. [ id:'test' ]
bam (file)
BAM/CRAM file
*.{bam,cram}
bai (file)
BAM index file. This is automatically found base on BAM input file name
*.{bai}
ref (file)
Reference fasta file
*.{fa, fasta, fas}
ref_fai (file)
Reference index file. This is automatically found based on referece input file name.
*.{.fai}
region_file (file)
File with a list of chromosome/locations in reference genome to genotype. One region per line in the format <chr>:<start>-<stop>. This or --region (in ext.args) must be specified.
*
Output
Name (Type)
Description
Pattern
meta (map)
Groovy Map containing sample information
e.g. [ id:'test' ]
