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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!


  • SChaluvadiSChaluvadi Member, Broadie, Moderator admin

    Definitely please retry with PL as Illumina since I don't believe there is support for BGIseq currently. Here is a ticket that was made to support this explicitly but it looks like our tools do support BGI sequencing data. Regarding uBAM generation, I would suggest using this tutorial since it has been most recently updated. If you could let us know what the results of changing PL look like, I think it might be easier to determine what could be happening with the sort order issues.

  • ibrahimkibrahimk Member

    I just got the results. Retrying with PL as illumina solved the error at the ValidateCram. I also did not coordinate order the uBam, it was the default queryname.

  • SChaluvadiSChaluvadi Member, Broadie, Moderator admin

    @ibrahimk Great! Glad to hear that you were able to solve the issue! Let us know if there is anything else we can help with.

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