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I'm evaluating replacing our pipeline from trimmomatic to fastp, but fastp is slower than trimmomatic.
fastp: 2:18.08
trimmomatic: 1:09.35
fastp command:
```bash
/usr/bin/time -v /path/to/fas…
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### Instructions
gatk --java-options "-Xmx12G -Djava.io.tmpdir=/data/nws/WES/1align_out/200919_A00682_0446_AHCVMJDSXY/tmp -DGATK_STACKTRACE_ON_USER_EXCEPTION=true" BaseRecalibrator -R /data/nws/WES/r…
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**Is your feature request related to a problem? Please describe.**
Currently, tracking of task states is (or will be) implemented by parsing `cwl-tes` logs in conjunction with polling of the relevant…
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### Description of the problem
Running different WES implementations, we ran into the issue that the definition of state `EXECUTOR_ERROR` is somewhat ambiguous.
The relevant states are [currentl…
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One issue with running gCNV properly and successfully (and perhaps other GATK tools that work with different data types) is that different data types requires running GATK using wildly different choic…
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## Product Briefs
- [Benefit content model](https://github.com/department-of-veterans-affairs/va.gov-team/blob/master/products/content/structured-content/benefits-content-model/README.md)
- [VA bene…
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Using GATK jar /usr/local/gatk-4.1.3.0/gatk-package-4.1.3.0-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_writ…
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I can generate a key and save it with `travis sshkey --generate`. However, when I attempt to reuse this key with another repository, I always seem to get this error message:
```
$ travis sshkey --upl…
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Hi,
I conducted a test on a dataset and generated my BAM and BAI files using 'samtools'. However, I encountered some errors during the process. I would appreciate any solutions you might have. A…