Generates a count of coverage of alleles
meta:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end
input:file
BAM/CRAM/SAM file
*.{bam,cram,sam}
input_index:file
BAM/CRAM/SAM index file
*.{bai,crai,sai}
loci:file
loci file
*.{tsv}
fasta:file
Input genome fasta file. Required when passing CRAM files.
allelecount
*.alleleCount:file
Allele count file
*.{alleleCount}
versions
versions.yml:file
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)
