Clips read alignments where they match BED file defined regions
Input
name:type
description
pattern
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
bam:file
BAM/CRAM/SAM file
*.{bam,cram,sam}
bed:file
BED file of regions to be removed (e.g. amplicon primers)
*.{bed}
save_cliprejects:boolean
Save filtered reads to a file
save_clipstats:boolean
Save clipping stats to a file
Output
name:type
description
pattern
bam
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.clipallowed.bam:file
Clipped reads BAM file
*.{bam}
stats
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.clipstats.txt:file
Clipping statistics text file
*.{clipstats.txt}
rejects_bam
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.cliprejects.bam:file
Filtered reads BAM file
*.{cliprejects.bam}
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.
