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