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Can funcotator remove mutation data from dbsnp #8636

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lh12565 opened this issue Dec 29, 2023 · 0 comments
Open

Can funcotator remove mutation data from dbsnp #8636

lh12565 opened this issue Dec 29, 2023 · 0 comments

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@lh12565
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lh12565 commented Dec 29, 2023

Hi, I use funcotator to call somatic mutations as below:

gatk Funcotator \
-R $ref/Homo_sapiens_assembly38.fasta \
-V ../${array[1]}.filter.vcf \
-O ${array[1]}.maf \
--output-file-format MAF \
--data-sources-path Funcotator_data/funcotator_dataSources.v1.7.20200521s/ \
--ref-version hg38 \
--annotation-default tumor_barcode:${array[1]} \
--annotation-default normal_barcode:${array[0]} 
done

Can funcotator remove the mutation data in dbsnp by default? or I need extra removal? Is there a parameter to remove these mutations?
Thanks!

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