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Issues about "Variant allele frequency/fraction and potential germlinevariants" #3

Open lincj1994 opened 3 years ago

lincj1994 commented 3 years ago

Hi. If I have performed data pre-processing step to filter out possiblegermline variants and only kept predicted somatic mutations, can the CBP2 of all variants be assigned a score of 1?

maxh190 commented 3 years ago

Hi Caijin,

I don't quite understand your question. Do you mean changing the current criteria?

Thanks, Max

On Thu, Jul 22, 2021 at 12:49 PM Caijin Lin @.***> wrote:

Hi. If I have performed data pre-processing step to filter out possiblegermline variants and only kept predicted somatic mutations, can the CBP2 of all variants be assigned a score of 1?

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lincj1994 commented 3 years ago

Thanks for your reply. The "VIC: VIC and Evidence" column in the VIC output didn't assign CBP2 and CBP3 for a variant if I didn't provide the corresponding evidence file. I dont know if I can assign CBP2 a score of 1 in the VIC output by myself if I know the variant is somatic and recalculate the total VIC score and change the pathogenicity level. I think it's more convenient to change the score in the VIC output than providing evidence file.

Here is an example in your vic_test1.hg19_multianno.txt.vic.

Chr Start   End Ref Alt Ref.Gene    Func.refGene    ExonicFunc.refGene  Gene.ensGene    avsnp150    clinvar: Clinvar    VIC: VIC and Evidence
7   55259515    55259515    T   G   EGFR    exonic  nonsynonymous SNV   ENSG00000146648 rs121434568  clinvar: 7      VIC: Uncertain significance EVS=[0, 1, NONE, NONE, 0, 0, 2, 2, 2, NONE]

If I know this variant is somatic, can I change the output manually into VIC: Uncertain significance EVS=[0, 1, 1, 1, 0, 0, 2, 2, 2, NONE] in Excel?

maxh190 commented 3 years ago

Providing additional information in your evidence file (tab-delimited text file) is up to your own evidence/knowledge. You may refer the evidence file in the example folder to re-run your analysis.