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Update purple and use hmftools v6_0 references #25

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skchronicles opened this issue Jan 23, 2025 · 0 comments
Open

Update purple and use hmftools v6_0 references #25

skchronicles opened this issue Jan 23, 2025 · 0 comments
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skchronicles commented Jan 23, 2025 •
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Purple failing with latest merged somatic call set

Purple is failing when provided the latest merged somatic call set with the SEQC TN pair. It errors out while parsing the input somatic VCF file with java type-casting errors.

Here is a screen shot of the error:
Image

At some point the program fail when try to type cast a list to a string.

To resolve the issue:

  1. Build a docker image with the latest version of hmtools dependencies for sage (needs latest version of java, needs R, and circos)
  2. Update to the latest jar file for hmftools purple (v4.0.2)
  3. Pass purple SAGE's filtered norm vcf file (purple does not like the latest merged VCF from multiple callers)
  4. Use the latest v6_0 resource bundle from hmftools: https://console.cloud.google.com/storage/browser/hmf-public/HMFtools-Resources/dna_pipeline/
@skchronicles skchronicles self-assigned this Jan 23, 2025
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