HiFi-based caller for highly homologous genes
meta
Groovy Map containing sample information e.g. [ id:'sample1', single_end:true ]
[ id:'sample1', single_end:true ]
bam
Sorted BAM file
*.bam
bai
Index of BAM file
*.bai
meta2
Groovy Map containing reference information e.g. [ id:‘genome’ ]
fasta
The reference fasta file
*.fasta
meta3
Groovy Map containing config information e.g. [ id:‘config’ ]
config
Config file
*.yaml
versions
File containing software versions
versions.yml
(re)aligned BAM file
*.paraphase.bam
Index of (re)aligned BAM file
*.paraphase.bam.bai
json
Summary of haplotype and variant calls
*.paraphase.json
vcf
VCF file(s) per gene
*.vcf
