Compresses VCF files
meta:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end
bam:file
Input BAM file
*.{bam}
intervals:file
Input intervals file. A file (commonly ‘.bed’) containing regions to subset
meta2:map
fasta:file
FASTA reference file
*.{fasta,fa}
save_mpileup:boolean
Save mpileup file generated by bcftools mpileup
vcf
*vcf.gz:file
VCF gzipped output file
*.{vcf.gz}
tbi
*vcf.gz.tbi:file
tabix index file
*.{vcf.gz.tbi}
stats
*stats.txt:file
Text output file containing stats
*{stats.txt}
mpileup
*.mpileup.gz:file
mpileup gzipped output for all positions
{*.mpileup.gz}
versions
versions.yml:file
File containing software versions
versions.yml
Generates genotype likelihoods at each genomic position with coverage.
