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