bams2crams
Format
cg bams2crams ?options? bamfile ?bamfile? ...
Summary
Convert bam files to a cram
Description
Converts all given bam files to cram. The resulting cramfiles will
have the same filename as the source bam, but with .cram instread of
.bam as file extension.
The command supports parallel processing using the joboptions
Arguments
- bamfile
- bamfile
Options
- -refseq file/dir
- file or directory containing the reference genome sequence
(this option must be given)
- -handlebam old/keep/rm
- what to do with the bam file (old) rename to file.old (is the
default), (keep) keep it as is, (rm) delete the bam file after
conversion
- -threads number
- use number of threads for the conversion
- -index 0/1
- if 1 (default), create the crai index of the cram file
Category
Format Conversion