processing steps to be on the lookout for in a CRAM?

[brettva]

Thank you for developing this tool. I have a collaborator that has some CRAMS that I might use as input for this caller. I see in the documentation that processing steps like bwa-postalt should be avoided. I am wondering are there any other obvious processing steps that I should be on the lookout for when evaluating whether these CRAMS are suitable as input for Cyrius?

Thank you

[xiao-chen-xc]

Hi @brettva I think it should be find as long as the post-processing steps do not change the MAPQ. I would recommend that you run a small set of samples first and check the call rate, i.e. samples that have a call instead of "None". If you see many samples have a "None" call, feel free to reach out to me and we can troubleshoot together.