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