Support for CRAM file?

[dr-ashu-geno]

Dear @ricardovialle

Does snakeSV support CRAM files too?

Every time I submit the job, it is canceled because BAMtools cannot index the CRAM file!

Any suggestion for this? Converting CRAM to BAM is both time and space consuming.

Thank you,

[ricardovialle]

Hi @dr-ashu-geno,

I'm sorry about that. I haven't actually tested CRAMs as input, but most SV callers can work with CRAMs. I might be able to work in the pipeline next week to have this fixed.

Thanks!

[dr-ashu-geno]

Dear @ricardovialle

Thank you for the reply.
It worked for me using two test BAM files but I had to give up using snakeSV as I have several thousands of samples in CRAM format and unfortunately it is not possible for me to convert each CRAM file to BAM format.

That will be very kind of you if you can let me know if it will be possible to use CRAM files as input whenever it is fixed!

Thanks!