Question about CRAM file support

[skchronicles]

Hey there,

I hope you are having a great day, and that all is going well on your side!

Thank you for creating and maintaining this amazing tool. I just have a really quick question. Does chromoscope currently support providing read alignments in CRAM format (.CRAM/.CRAI)? I see throughout the documentation references to optionally providing a BAM file but I did not see anything reference/mention CRAM files. This could potentially be useful from a cost-saving/disk-savings perspective, especially if data is being stored in S3.

Please let me know what you think, and have an awesome day!

Best regards,
Skyler Kuhn

[sehilyi]

Hi @skchronicles, Thank you for reaching out, and happy new year!

It is correct that CRAM is not supported at the moment. I will discuss this with the team this week to plan the implementation and follow up with you.

[skchronicles]

@sehilyi Okay, that sounds amazing! Thank you for looking into this issue.