GenomeComb

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