Reports alignment summary statistics for a BAM/CRAM/SAM file
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}
bai:file
Index for BAM/CRAM/SAM file
*.{bai,crai,sai}
Output
name:type
description
pattern
idxstats
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.idxstats:file
File containing samtools idxstats output
*.{idxstats}
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.
