1. Community
2. Germline
3. Input configuration for GATK4-gCNV workflow on Terra

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
• November 29, 2022 10:15
• 0 votes

1. Community
2. Somatic
3. Fake panel of normal performs better than publicly available in variant calling tumor-only samples

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
• June 02, 2020 13:46
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1. Community
2. Somatic
3. Fake panel of normal performs better than publicly available in variant calling tumor-only samples

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
• May 21, 2020 07:26
• 0 votes