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aradenbaugh / radia

RADIA: RNA and DNA Integrated Analysis for Somatic Mutation Detection
GNU Affero General Public License v3.0
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Germline filter #5

Closed Hecate08 closed 7 years ago

Hecate08 commented 8 years ago

Hello,

We are running RADIA on 6 human samples. But after all the filter steps there were many variants, which have a high alternative allele frequency in the normal DNA. How do I know if the germline filter is applied or not?

Thanks Hecate

aradenbaugh commented 8 years ago

Hi Hecate,

Are you looking at the passing somatic variants? They should have a PASS in the filter column, and SS=2 in the FORMAT column, and the word SOMATIC in the INFO column. The germline calls will have SS=1 and will not contain the word SOMATIC in the INFO column. There will be many passing germline variants.

Thanks, Amie