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Surprising Alignment

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  • Surprising Alignment

    Hi,

    I have been working with some WES files and getting surprising results, in which very rare variants are being found much more often than I would expect. The original files have been aligned but there are single tracks which don't look, from viewing on IGV, like they have been placed in the correct place. I have converted them to fastq files and then re-aligned with the same results. I have included a screenshot from IGV with the same locus from the original alignment. Can anyone give me some direction as to whether this is normal? After I carry out Variant Calling (GATK Best Practices), I am being left with some quite unlikely de novo variants as a result.

    Many Thanks for any responses, I will provide further information if required.

    Here is a link the the image:
    https://photos.app.goo.gl/LGEDVbpCMh87USCq7
    Last edited by drr719; 03-23-2022, 06:07 AM. Reason: link
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