1. Technical Documentation
2. Algorithms
3. Base Quality Score Recalibration (BQSR)

Hi I have a question. In the description of this process, the BaseRecalibrator tool requires databases of known polymorphisms to recalibrate the quality of the bases. As explained in this document,...

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• Adrián Segura
• April 17, 2021 11:57
• 1 vote

1. Community
2. Non-Human
3. VQSR: how is insufficient variance inferred for annotations?

Thanks Genevieve, I have already managed to download the vcfs files exposed in the examples, however, since I want to detect somatic mutations on tumor samples, should I also consider providing fil...

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• Adrián Segura
• April 17, 2021 14:03
• 0 votes

1. Tool Index
2. 4.1.3.0
3. VariantRecalibrator

In case of wanting to detect oncological variants on tumor samples, what databases should I provide as --resource? Is it convenient to select vcfs from specific databases like COSMIC? Or is it bett...

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• Adrián Segura
• April 17, 2021 13:54
• 0 votes

1. Tool Index
2. 4.1.4.1
3. GetPileupSummaries

In case of wanting to detect somatic variants of tumor samples, is it convenient to provide the tool (in -V or -L) with database files specialized in somatic mutations such as COSMIC?

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• Adrián Segura
• April 17, 2021 12:42
• 0 votes

1. Community
2. Non-Human
3. VQSR: how is insufficient variance inferred for annotations?

Hello, I am trying to execute the same operation for the hg19 reference, however it is difficult for me to find the files that you mention in your code (resource files). Can you tell me where to fi...

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• Adrián Segura
• April 05, 2021 16:32
• 0 votes