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