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varscan2 output can't be fed to snpEff. ID column missing? #66

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gabrielet opened this issue Feb 2, 2024 · 0 comments
Open

varscan2 output can't be fed to snpEff. ID column missing? #66

gabrielet opened this issue Feb 2, 2024 · 0 comments

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@gabrielet
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gabrielet commented Feb 2, 2024

anyone has encountered this error while running snpEff using a somatic varscan output?

apparently, there is column missing in the output of varscan.

thank you for any hint on how to solve.

EDIT, in case it is needed, here the code:

java -Xmx8g -jar /home/user/genomics/snpEff/snpEff.jar \
        -c /home/user/genomics/snpEff/snpEff.config \
        -v database \
        /home/user/data-02/comparison_results/varscan_results/somatic/varscan_output.txt.indel \
        > my_annotations

-v database is a database that is precompiled. nothing exotic there.

@gabrielet gabrielet changed the title varscan2 output can be fed to snpEff. ID column missing? varscan2 output can't be fed to snpEff. ID column missing? Feb 2, 2024
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