Yuanyuan Wu
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Latest activity by Yuanyuan Wu-
Yuanyuan Wu commented,
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 commented,
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 commented,
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 commented,
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 created a post,
Sample does not have a non-negative sample median when running DenoiseReadCounts to test the example data Tutorial11682
Using GATK jar /gatk/gatk-package-4.1.2.0-local.jarThe Genome Analysis Toolkit (GATK) v4.1.2.0HTSJDK Version: 2.19.0Picard Version: 2.19.0 Command: gatk --java-options "-Xmx16G" DenoiseReadCounts...