bam2cram
Format
cg bam2cram ?options? bamfile ?cramfile?
Summary
Convert a bam file to a cramfile
Arguments
- bamfile
- bamfile
- cramfile
- (result) cramfile, if not given, the result will have the
same filename as the source, but with .cram instread of .bam as
file extension
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.
- -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