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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

GetPileupSummaries

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    Pamela Bretscher

    Hi Mommy Misato,

    It seems like this may be an issue with the naming of the chromosomes in your files. Could you please check the naming conventions between your files to ensure that they match? Here is an article about mismatching references that may be useful: https://gatk.broadinstitute.org/hc/en-us/articles/360035891131-Errors-about-input-files-having-missing-or-incompatible-contigs

    Kind regards,

    Pamela

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    Mommy Misato

    We thought that was the cause when we were using the ref 37 so we switched to the 38 and it still gave me the same error message. 

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    Pamela Bretscher

    Hi Mommy Misato,

    It is common for some files to use "Chr1" and others to use just "1" for the naming convention, which can lead to errors. Did you check that the files have matching references? If all of the references match, you may need to recreate your sequence directory to see if this solves the problem. 

    Kind regards,

    Pamela

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    Mommy Misato

    Yeah, I checked that all the references matched and we also started over and recreated or directory and index. I've literally tried everything. ref 37 is chr1 and ref 38 is 1

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    Pamela Bretscher

    Mommy Misato,

    Okay, thank you for clarifying. Could you please share your full stack trace and the portion of the sequence dictionary file containing Chr1? 

    Thank you,

    Pamela

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