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