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Why do I see that the guide for `CreateSomaticPanelOfNormals` is `FilterMutectCalls` not used after calling germline `Mutect2` variants? Is this just a suggestion, and how strong is that suggestion...

• AMN
• September 10, 2021 16:17
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I have what i believe to be unstranded RNA data, and when I ran CollectRnaseqMetrics with STRAND=NONE I got absolutely no strandedness metrics, which I would need to confirm that my sample is indee...

• AMN
• July 02, 2021 16:45
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I am seeing a different result when i use ApplyBQSR vs ApplyBQSRSpark, using the exact same inputs. I tried with both GATK 4.1.0.0 and 4.1.9.0 i am comparing the command: gatk ApplyBQSR      --java...

• AMN
• April 22, 2021 15:40
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GATK version: 4.1.0.0 and 4.1.9.0Comparing two processes:``` gatk MarkDuplicates \       --TMP_DIR ./ \       --MAX_RECORDS_IN_RAM 50000 \       --INPUT ${inputBam} \       --METRICS_FILE ${idSampl...

• AMN
• January 20, 2021 00:36
• Edited
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