Pedro Miguel Raposo
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Recent activity by Pedro Miguel Raposo Sort by recent activity-
Create Somatic PON threshold
AnsweredHello GATK Team, I have a simple question when it comes to creating a somatic PON. Under the 'CreateSomaticPanelOfNormals' description it says that "The tool takes multiple normal sample callsets p...
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Custom made Panel of Normals required?
Hello, For what I understand, the GATK's best practices recommends the usage of a Panel of Normals (PON) for an accurate somatic mutation detection. By having a large enough pool of "normal" sample...
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Sample intervals must be identical to the original intervals used to build the panel of normals
Hi. When I follow the CNV pipeline (https://gatkforums.broadinstitute.org/gatk/discussion/11682#2) I got the following error, whilst running the DenoiseReadCounts function: "Sample intervals must b...
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java.lang.IllegalArgumentException: Records contained at least one interval that did not validate against the sequence dictionary.
Hello.Whilst counts coverage of paired end fragments, using the CollectReadCounts function (GATK v. 4.1.3.0), I got the following an error. It states: java.lang.IllegalArgumentException: Records co...