Add localization optional to varscan somatic. #79
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The varscan helper image is much slimmer!
chrisamiller
approved these changes
Jan 25, 2023
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Varscan variant calling seems to be working based on the final outputs. |
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This required building a newer image with varscan and a newer samtools that supports reading
gs://URLs.There are some differences in the varscan output as a result of this change. The most dramatic change comes not from upgrading to 1.16.1 but from switching from the custom samtools 1.3.1/htslib 1.3.2 combo in the CLE image to any other version I tried (1.3.1 and 1.7). So not sure if there's something special about the combination in the CLE image...
This is part of #64.