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Variant Discovery in High-Throughput Sequencing Data

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Funcotator Misconfigured Error (All IGR Annotations)

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    Gus Fridell

    I was able to determine from aligning the bed file with the ucsc genome browser that the coordinates are in hg38.

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    Genevieve Brandt (she/her)

    Hi Gus Fridell,

    This looks like you have an issue with your resource files mismatching in terms of their reference versions. There are usually more differences between hg38 and GRCH38 than just changing the naming from "chr1" to "1". I would recommend looking more closely to determine that your reference versions are consistent. For changing reference versions, we recommend the LiftOver tool to be sure that all the information is changed properly.

    I would also recommend that you update your Funcotator data sources because there were some issues in the 1.7 data sources I believe.

    Please let me know if you have any other questions.

    Best,

    Genevieve

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    Gus Fridell

    Hi Genevieve, 

    Thanks for your response! What data resource do you recommend using? I checked the google share and the ftp server, and based on the filenames, v1.7 are the latest (2020).

    I will try to investigate the references more. 

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    Genevieve Brandt (she/her)

    Yeah, it does look like the latest published online. It might have just been an issue with the somatic data sources. The person I would need to ask about this is on vacation for a couple weeks, so I'll find out and get back to you in a few weeks.

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    Gus Fridell

    Thank you, Genevieve.

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    Genevieve Brandt (she/her)

    Hi Gus Fridell,

    I have followed up with my co-worker and have some notes you should consider:

    • The data sources should be fine, you're using the most up to date version of the germline data sources.
    • Our data sources all have hg38 and GRCH38 using "chr1", not "1". So the reference genome you initially used for calling might be different than the data sources, which is why you are running into this issue. 
    • Take a look at the reference you used for the initial calling and either do a LiftOver or you can create funcotator data sources for the reference genome used.

    Let me know if you have any other questions.

    Best,

    Genevieve

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