Sort SAM/BAM/CRAM file
meta
Groovy Map containing sample information e.g. [ id:‘test’, single_end
bam
BAM/CRAM/SAM file(s)
*.{bam,cram,sam}
meta2
Groovy Map containing reference information e.g. [ id:‘genome’ ]
fasta
Reference genome FASTA file
*.{fa,fasta,fna}
Sorted BAM file
*.{bam}
cram
Sorted CRAM file
*.{cram}
crai
CRAM index file (optional)
*.crai
csi
BAM index file (optional)
*.csi
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.
