Generates a count of coverage of alleles
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
input{:bash}
:file
BAM/CRAM/SAM file
*.{bam,cram,sam}
input_index{:bash}
BAM/CRAM/SAM index file
*.{bai,crai,sai}
loci{:bash}
loci file
*.{tsv}
fasta{:bash}
Input genome fasta file. Required when passing CRAM files.
allelecount{:bash}
*.alleleCount{:bash}
Allele count file
*.{alleleCount}
versions{:bash}
versions.yml{:bash}
File containing software versions
versions.yml
Takes a file of locations and a [cr|b]am file and generates a count of coverage of each allele at that location (given any filter settings)
