filter/convert SAM/BAM/CRAM file
meta
Groovy Map containing sample information e.g. [ id:‘test’, single_end
input
BAM/CRAM/SAM file
*.{bam,cram,sam}
index
BAM.BAI/BAM.CSI/CRAM.CRAI file (optional)
*.{.bai,.csi,.crai}
meta2
Groovy Map containing reference information e.g. [ id:‘test’ ]
fasta
Reference file the CRAM was created with (optional)
*.{fasta,fa}
qname
Optional file with read names to output only select alignments
*.{txt,list}
bam
optional filtered/converted BAM file
*.{bam}
cram
optional filtered/converted CRAM file
*.{cram}
sam
optional filtered/converted SAM file
*.{sam}
bai
optional BAM file index
*.{bai}
csi
optional tabix BAM file index
*.{csi}
crai
optional CRAM file index
*.{crai}
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.
