GenomeComb

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