BAM
meta
Groovy Map containing sample information e.g. [ id:‘test’, single_end
input
BAM/CRAM/SAM file
*.{bam,cram,sam}
fasta
FASTA reference file
*.{fasta,fa}
intervals
Interval FILE
*.bed
mpileup
mpileup file
*.{mpileup}
versions
File containing software versions
versions.yml
SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA.
