SNP and Indel variant caller on a per-locus basis
meta:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
bam:file
Sorted and indexed BAM/CRAM/SAM file
*.bam
bai:file
BAM index file
*.bai
meta2:map
Groovy Map containing reference information. e.g. [ id:‘test’, single_end:false ]
fasta:file
Reference file used to generate BAM file
.{fasta,fa,fna}
meta3:map
fai:file
Index of reference file used to generate BAM file
.fai
meta4:map
dict:file
GATK dict file for reference
.dict
meta5:map
intervals:file
Bed file with the genomic regions included in the library (optional)
*.intervals
meta6:map
Groovy Map containing file meta-information for the contamination file. e.g. [ id:‘test’, single_end:false ]
contamination:file
Tab-separated file containing fraction of contamination in sequencing data (per sample) to aggressively remove
*
meta7:map
Groovy Map containing file meta-information for the dbsnps file. e.g. [ id:‘test’, single_end:false ]
dbsnp:file
VCF file containing known sites (optional)
meta8:map
Groovy Map containing file meta-information for the VCF comparison file. e.g. [ id:‘test’, single_end:false ]
comp:file
Comparison VCF file (optional)
vcf
*.vcf.gz:file
VCF file containing called variants
*.vcf.gz
versions
versions.yml:file
File containing software versions
versions.yml
The full Genome Analysis Toolkit (GATK) framework, license restricted.
