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uBam ordering confusion & BGISEQ-500 platform
Hi FireCloud team!
First off, thanks a lot for this great platform and tools!
According to the tutorial here (https://tinyurl.com/y49aecfy), during uBam generation I should not touch the SORT_ORDER which is by default queryname. And this is what I had done. However, I have also seen this article (https://tinyurl.com/y55jq9q7) which clearly states that the uBam needs to be coordinate ordered. Can you please just clarify this part to me?
My goal is to input in PE WES data generated by BGISEQ-500 platform into the 5 dollars genome analysis workflow. I did an initial try. And I think it almost worked perfectly fine, except the final ValidateCram part. I believe that it happened due to my PL=BGI definition during uBam generation. Any other reasons that it might have happened? Here is the error:
message: Job germline_single_sample_workflow.ValidateCram:NA:1 exited with return code 3 which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details.
I am planning to regenerate the uBam with PL=ILLUMINA description, however I wanted to also double check with you guys on the SORT_ORDER part of the code.
Thanks a lot!