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