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Variant Discovery in High-Throughput Sequencing Data

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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

PlotModeledSegments: java.lang.IllegalArgumentException: Records were not strictly sorted in dictionary order.

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    Gökalp Çelik

    Hi Beetle

    Any of those input files may be out of order. During combine stage it is possible that some of those contigs got sorted lexicographically however that order should be exactly the same as the one in the sequence dictionary. 

    Since we don't have access to your files we cannot recreate this problem in our hands. 

    If you think this is a bug and report a detailed bug report we recommend you to follow the steps in the below article and submit data that we can check and try to recreate the bug.

    https://gatk.broadinstitute.org/hc/en-us/articles/360035889671-How-do-I-submit-a-detailed-bug-report 

    I hope this helps.

    Regards. 

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    Beetle

    Hi Gökalp Çelik

    Thanks a lot for your reply. I have uploaded all the input files. I think they are in dictionary order. Can you please take a look. Thanks a lot for your help. Download files here:  

     

     

     

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    Gökalp Çelik

    Hi Beetle

    Can you upload these files to the ftp that we provide in the article? We are unable to reach any user defined environment due to security reasons. 

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    Beetle

    Hi Gökalp Çelik

     

    I was able to upload file following instructions from here. https://gatk.broadinstitute.org/hc/en-us/articles/360035889671-How-do-I-submit-a-detailed-bug-report#article-comments

    please check file name: put input_files.tar.gz

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    Gökalp Çelik

    Hi again. 

    Your denoised copy ratio file contains inputs from contigs that are not in the main chromosomes. All other files end up with chrY but this file goes beyond those contigs. Can you remove those entries and try again to see if the issue persists?

    Regards. 

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    Beetle

    thanks. you were wright. There was some problem with my denoized file. I was able to fix it. thanks. 

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