Lofreq subcommand to call low frequency variants from alignments
meta:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end
bam:file
BAM input file
*.{bam}
intervals:file
BED file containing target regions for variant calling
*.{bed}
fasta:file
The reference fasta file
vcf
*.vcf.gz:file
VCF output file
*.{vcf}
versions
versions.yml:file
File containing software versions
versions.yml
A fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data
