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mskcc / tempo

CCS research pipeline to process WES and WGS TN pairs
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emit original quals #1008

Closed anoronh4 closed 7 months ago

anoronh4 commented 7 months ago

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.

gongyixiao commented 7 months ago

please leave the compression level changes as a separate PR if we need it.