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 files: old: rename to file.old (is
the default). keep: keep it as is. rm: delete the bam file after
conversion.
- -links ignore/rename/convert/error
- What to do with soft links: rename (default): rename the link
and the place it is pointing too, it will not convert the file it
is/was pointing to. convert: rename and convert the file pointed to
(even if it is outside the directory that is being renamed).
ignore: do nothing with it. error: give an error.
- -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