Perform joint genotyping on one or more samples pre-called with HaplotypeCaller.
meta:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end
input:file
gVCF(.gz) file or a GenomicsDB
*.{vcf,vcf.gz}
gvcf_index:file
index of gvcf file, or empty when providing GenomicsDB
*.{idx,tbi}
intervals:file
Interval file with the genomic regions included in the library (optional)
intervals_index:file
Interval index file (optional)
meta2:map
Groovy Map containing fasta information e.g. [ id:‘test’ ]
fasta:file
Reference fasta file
*.fasta
meta3:map
Groovy Map containing fai information e.g. [ id:‘test’ ]
fai:file
Reference fasta index file
*.fai
meta4:map
Groovy Map containing dict information e.g. [ id:‘test’ ]
dict:file
Reference fasta sequence dict file
*.dict
meta5:map
Groovy Map containing dbsnp information e.g. [ id:‘test’ ]
dbsnp:file
dbSNP VCF file
*.vcf.gz
meta6:map
Groovy Map containing dbsnp tbi information e.g. [ id:‘test’ ]
dbsnp_tbi:file
dbSNP VCF index file
*.tbi
vcf
*.vcf.gz:file
Genotyped VCF file
tbi
*.tbi:file
Tbi index for VCF file
versions
versions.yml:file
File containing software versions
versions.yml
Genome Analysis Toolkit (GATK4)
