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wustl-oncology / analysis-wdls

Scalable genomic analysis pipelines, written in WDL
MIT License
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Add localization optional to varscan somatic. #79

Closed tmooney closed 1 year ago

tmooney commented 1 year ago

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.

malachig commented 1 year ago

Varscan variant calling seems to be working based on the final outputs.