Add CRAM support

[marchoeppner]

Currently, the pipeline uses "*.bam" to find input files. We have, for a while now, switched to CRAM since the space savings are significant (50%). Any chance that the pipeline could be updated to natively support cram (DV does, as far as I know)?

[PhilPalmer]

Hi @marchoeppner,

Currently, the pipeline uses "*.bam" to find input files.

This is only when using the --bam_folder parameter.

You could try using to the --bam parameter to specify the path to your CRAM file (as this doesn't check the file extension).

However, I suspect the preprocess_bam process will fail as this was meant to preprocess BAM files only.

Support for CRAM files was added in DeepVariant v0.7.0. So, in theory, the pipeline should support it. However, in practice, I doubt that it will. This hasn't been tested, I think the script will need changing and I know that there have been improvements for CRAM support in later DeepVaraint versions.