mariesmith
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Latest activity by mariesmith-
mariesmith commented,
Hi, I am not able to find those files for hg38 in the provided bucket gs://gatk-best-practices/cnv-germline-pipeline nor in https://console.cloud.google.com/storage/browser/gcp-public-data--broad-r...
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mariesmith commented,
Hello David, thanks for your response! Unfortunately, we do not have a proper way to check if they are germline variants as we do not have access to normal-matched samples. We check probe size and ...
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mariesmith commented,
Dear GATK team, Thanks for your response. We did not include a germline resource as we are interested in detecting all possible variants. The commands used are the following: gatk Mutect2 \ ...
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mariesmith created a post,
Fake panel of normal performs better than publicly available in variant calling tumor-only samples
Dear GATK team, We are working with tumor-only samples using Mutect2 and FilterMutectCalls and we are analyzing confirmed PCR variants when changing the panel of normals. Unfortunately, we do no...