Lofreq subcommand to for insert base and indel alignment qualities
meta
Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]
[ id:'sample1', single_end:false ]
bam
Sorted BAM/CRAM/SAM file
*.{bam,cram,sam}
fasta
Reference genome FASTA file
*.{fasta}
versions
File containing software versions
versions.yml
BAM/CRAM/SAM file with base and indel alignment qualities
A fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data