Merge BAM or CRAM file
meta
Groovy Map containing sample information e.g. [ id:‘test’, single_end
input_files
BAM/CRAM file
*.{bam,cram,sam}
meta2
Groovy Map containing reference information e.g. [ id:‘genome’ ]
fasta
Reference file the CRAM was created with (optional)
*.{fasta,fa}
meta3
fai
Index of the reference file the CRAM was created with (optional)
*.fai
bam
BAM file
*.{bam}
cram
CRAM file
*.{cram}
versions
File containing software versions
versions.yml
csi
BAM index file (optional)
*.csi
crai
CRAM index file (optional)
*.crai
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.