Produces comprehensive statistics from SAM/BAM/CRAM file
meta
Groovy Map containing sample information e.g. [ id:‘test’, single_end
input
BAM/CRAM file from alignment
*.{bam,cram}
input_index
BAI/CRAI file from alignment
*.{bai,crai}
meta2
Groovy Map containing reference information e.g. [ id:‘genome’ ]
fasta
Reference file the CRAM was created with (optional)
*.{fasta,fa}
stats
File containing samtools stats output
*.{stats}
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.