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