bam_index
Format
cg bam_index ?options? bamfile ?bamfile? ...
Summary
index a bam/cram/sam file.
Description
Indexes the given bam/cram/sam files using samtools index, but
with improvements:
- index file will only be put in place when completed (so no
corrupted index file when e.g. interrupted)
- index file will get the same time as indexed bam file (reruns
will not unnecessarily cause reanalysis of everything dependent on
bam when you add indexes later)
- supports joboptions
Arguments
- bamfile
- bam file to index
Options
- -threads number
- number of threads to use for indexing
Category
Conversion