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Call Molecular Subtype for new PNOC samples #210

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runjin326 opened this issue Sep 22, 2021 · 1 comment
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Call Molecular Subtype for new PNOC samples #210

runjin326 opened this issue Sep 22, 2021 · 1 comment
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@runjin326
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What data file(s) does this issue pertain to?

histologies.tsv

What release are you using?

v10
SNV, fusion, CNV, mutation, GISTIC, focal CN and TP53 scores file.

Put your question or report your issue here.

Please call molecular subtype for new PNOC samples with following step

  1. Once the PR for updating molecular-subtyping-HGG module is merged (HGG Module Update PART2 OpenPedCan-analysis#121) are in, run new PNOC samples through molecular-subtyping-HGG module first.

  2. After the PR about subtyping correction/integration based on pathology dx (Molecular subtyping pathology update OpenPedCan-analysis#122) is in, run through molecular-subtyping-pathology, and merge the compiled_molecular_subtypes_with_clinical_pathology_feedback_and_report_info.tsv generated with the OpenPBTA v21 compiled_molecular_subtypes_with_clinical_pathology_feedback_and_report_info.tsv.

  3. Once PR for subtyping integration (Molecular subtype integrate module update OpenPedCan-analysis#123) is in, run everything through molecular-subtyping-integrate and get subtyping information for PNOC samples.

@runjin326 runjin326 self-assigned this Sep 22, 2021
@runjin326 runjin326 mentioned this issue Sep 22, 2021
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@runjin326 runjin326 added the v10 label Sep 22, 2021
@runjin326
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Closing with PR136 merged.

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