Compresses VCF files
meta
Groovy Map containing sample information e.g. [ id:‘test’, single_end
bam
Input BAM file
*.{bam}
intervals
Input intervals file. A file (commonly ‘.bed’) containing regions to subset
Groovy Map containing information about the genome fasta, e.g. [ id: ‘sarscov2’ ]
fasta
FASTA reference file
*.{fasta,fa}
save_mpileup
Save mpileup file generated by bcftools mpileup
vcf
VCF gzipped output file
*.{vcf.gz}
tbi
tabix index file
*.{vcf.gz.tbi}
stats
Text output file containing stats
*{stats.txt}
mpileup
mpileup gzipped output for all positions
{*.mpileup.gz}
versions
File containing software versions
versions.yml
Generates genotype likelihoods at each genomic position with coverage.
