Compresses VCF files
meta
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
bam
:file
Input BAM file
*.{bam}
intervals_mpileup
Input intervals file. A file (commonly ‘.bed’) containing regions to subset used by mpileup
intervals_call
Input intervals file. A file (commonly ‘.bed’) containing regions to subset used by call but need a fourth column with REF,ALT
meta2
fasta
FASTA reference file
*.{fasta,fa}
fai
FASTA reference file index
*.fai
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_bcftools
${task.process}
:string
The process the versions were collected from
bcftools
The tool name
bcftools --version | sed '1!d; s/^.*bcftools //'
The command used to generate the version of the tool
versions
Generates genotype likelihoods at each genomic position with coverage.
