emit original quals #1008
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emit original quals #1008
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please leave the compression level changes as a separate PR if we need it. |
gongyixiao
approved these changes
Apr 12, 2024
johnoooh
approved these changes
Apr 12, 2024
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Addressing #947
If we want to offset the increase in bam size that will result from this change we can use the following option to change the compression level:
--java-options "-Dsamjdk.compression_level=3". i think the default compression level is 2 for gatk, and the higher the compression level the smaller the bam (and the longer other analyses will take). that change is not in the PR yet, but i'm happy to add it.