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