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Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
Debug message from htsjdk.samtools.FixBAMFile
I use htsjdk.samtools.FixBAMFile to fix occasional bin errors when use BWA-backtrack with old datasets:
java -cp htsjdk.jar htsjdk.samtools.FixBAMFile source.bam fixed.bam
This bin fixing issue is discussed in more details here:
When I use an old htsjdk version (i.e. htsjdk-1.133.jar) it fixes bam files without any messages. When I use the newer htsjdk versions (e.g. htsjdk-2.4.1.jar or htsjdk-2.7.0.jar) they apparently do the job, but report a debug message like the following:
DEBUG 2016-11-02 20:03:38 BlockCompressedOutputStream Using deflater: Deflater
What is this message about? Is it OK to use the versions producing such message?