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