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3. CollectAllelicCounts interval_list

Dear GATK Team, I downloaded data from the following link. But it's different from the interval list example as the interval list "chr17_theta_snps.interval_list" showed  gatk --java-options "-Xmx3...

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• Yuanyuan Wu
• February 08, 2021 14:27
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3. Sample does not have a non-negative sample median when running DenoiseReadCounts to test the example data Tutorial11682

Ok, great. Thanks for your clarification. I need to run CollectReadCounts on the tumor samples from my own project anyway, am I right? Except for that, I got two other errors when I plot figures by...

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• Yuanyuan Wu
• January 15, 2021 21:09
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3. Sample does not have a non-negative sample median when running DenoiseReadCounts to test the example data Tutorial11682

Please see below, which I got after ran CollectReadCounts. How could I examine the count file to verify if that is true? Using GATK jar /gatk/gatk-package-4.1.2.0-local.jarRunning:java -Dsamjdk.use...

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• Yuanyuan Wu
• January 14, 2021 23:32
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3. Sample does not have a non-negative sample median when running DenoiseReadCounts to test the example data Tutorial11682

Yes, I can confirm that. The only difference is I used "CollectReadCounts" instead of "CollectFragmentCounts" because the GATK version is different. The previous steps:  gatk --java-options "-Xmx1...

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• Yuanyuan Wu
• January 13, 2021 19:33
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