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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

Contig chr1_KQ031383v1_fix not present in the sequence dictionary

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    Genevieve Brandt (she/her)

    Hi zzh,

    This error indicates that the reference versions of your files do not match. There is a contig chr1_KQ031383v1_fix in one of your files that seems to be a non-standard contig name, so I would start there to make sure it matches your resource files.

    Please let me know if you have any further questions.

    Best,

    Genevieve

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    zzh

    Hello, Genevieve
    Is there something wrong with my fastQC header file, causing the BAM file to appear chr1_KQ031383v1_fix in BAM file? Should I change the fastQC file and do it again

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    Genevieve Brandt (she/her)

    I think that there are reads in your BAM file mapped to chr1_KQ031383v1_fix, which is why the program almost runs to completion (you can see the status when looking at the Progress Meter). 

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    zzh

    Hello, Genevieve

    How can I solve this problem

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    Genevieve Brandt (she/her)

    It depends how the contig ended up in your bam file.

    One way would be to re-run BWA on your unmapped reads and make sure you are using the standard hg38. Here is the information about our resources: https://gatk.broadinstitute.org/hc/en-us/articles/360035890811-Resource-bundle

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