Replacing BAM with CRAM Files

Question

[joe_genome]

I'm starting to explore mapped sequence data formats. Specifically the possibility of replacing bam files with cram files, as bam and/or ubam files are generally quite heavy. Thus can affect transfer and computational times used in my linux systems.

However I wanted to know if other users have any experience with similar situations where the cram files will closely resemble the original bam/ubam files. In other words, can cram files be used as alternative to bam/ubam files in the input analysis.

[GenoMax]

can cram files be used as alternative to bam/ubam files in the input analysis.

Not as a general replacement far as I know. You may be able to pipe them in to some tools by converting them on fly using samtools. A quick scan seems to indicate that Picard tools and IGV can natively understand CRAM files.

[joe_genome]

Hey thanks for the clarification, was wondering if I could convert CRAM to BAM with samtools then?

[i.sudbery]

yes, samtools view can convert CRAM files to BAM.