Deprecate SHH TP53 subtyping

#247 was closed

analyses/README.md

@@ -29,7 +29,7 @@ Note that _nearly all_ modules use the harmonized clinical data file (`pbta-hist
 | [`molecular-subtyping-chordoma`](https://github.com/AlexsLemonade/OpenPBTA-analysis/tree/master/analyses/molecular-subtyping-chordoma) | `analyses/focal-cn-file-preparation/results/consensus_seg_annotated_cn_autosomes.tsv.gz` <br> `pbta-gene-expression-rsem-fpkm-collapsed.stranded.rds` | *In progress*; identifying poorly-differentiated chordoma samples per [#250](https://github.com/AlexsLemonade/OpenPBTA-analysis/issues/250) | N/A
 | [`molecular-subtyping-embryonal`](https://github.com/AlexsLemonade/OpenPBTA-analysis/tree/master/analyses/molecular-subtyping-embryonal) | `analyses/fusion-summary/fusion_summary_embryonal_foi.tsv` <br>  `pbta-histologies.tsv` <br> `pbta-sv-manta.tsv.gz` <br> `analyses/focal-cn-file-preparation/consensus_seg_annotated_cn_x_and_y.tsv.gz` <br> `analyses/focal-cn-file-preparation/cnvkit_annotated_cn_x_and_y.tsv.gz` <br> `analyses/focal-cn-file-preparation/controlfreec_annotated_cn_x_and_y.tsv.gz` <br> `pbta-gene-expression-rsem-fpkm-collapsed.stranded.rds` <br> `pbta-gene-expression-rsem-fpkm-collapsed.polya.rds` | *In progress*; molecular subtyping of non-medulloblastoma, non-ATRT embryonal tumors [#251](https://github.com/AlexsLemonade/OpenPBTA-analysis/issues/251) | N/A
 | [`molecular-subtyping-HGG`](https://github.com/AlexsLemonade/OpenPBTA-analysis/tree/master/analyses/molecular-subtyping-HGG) | `pbta-snv-consensus-mutation.maf.tsv.gz` <br> `analyses/focal-cn-preparation/results/cnvkit_annotated_cn_autosomes.tsv.gz` <br> `pbta-fusion-putative-oncogenic.tsv` <br> `pbta-cnv-cnvkit-gistic.zip` <br> `pbta-gene-expression-rsem-fpkm-collapsed.stranded.rds` <br> `pbta-gene-expression-rsem-fpkm-collapsed.polya.rds` | *In progress*; molecular subtyping of high-grade glioma samples [#249](https://github.com/AlexsLemonade/OpenPBTA-analysis/issues/249) | N/A
-| [`molecular-subtyping-SHH-tp53`](https://github.com/AlexsLemonade/OpenPBTA-analysis/tree/master/analyses/molecular-subtyping-SHH-tp53) | `pbta-histologies` <br> `pbta-snv-consensus-mutation.maf.tsv.gz` | Identify the SHH-classified medulloblastoma samples that have TP53 mutations | N/A
+| [`molecular-subtyping-SHH-tp53`](https://github.com/AlexsLemonade/OpenPBTA-analysis/tree/master/analyses/molecular-subtyping-SHH-tp53) | `pbta-histologies` <br> `pbta-snv-consensus-mutation.maf.tsv.gz` | *Deprecated*; Identify the SHH-classified medulloblastoma samples that have TP53 mutations [#247](https://github.com/AlexsLemonade/OpenPBTA-analysis/issues/247) | N/A
 | [`mutational-signatures`](https://github.com/AlexsLemonade/OpenPBTA-analysis/tree/master/analyses/mutational-signatures) | `pbta-snv-consensus-mutation.maf.tsv.gz` | Performs COSMIC and Alexandrov et al. mutational signature analysis using the consensus SNV data | N/A
 | [`mutect2-vs-strelka2`](https://github.com/AlexsLemonade/OpenPBTA-analysis/tree/master/analyses/mutect2-vs-strelka2) | `pbta-snv-mutect2.vep.maf.gz` <br> `pbta-snv-strelka2.vep.maf.gz` | *Deprecated*; comparison of only two SNV callers, subsumed by `snv-callers` | N/A
 | [`oncoprint-landscape`](https://github.com/AlexsLemonade/OpenPBTA-analysis/tree/master/analyses/oncoprint-landscape) | `pbta-snv-consensus-mutation.maf.tsv.gz` <br> `pbta-fusion-putative-oncogenic.tsv` <br> `analyses/focal-cn-file-preparation/results/controlfreec_annotated_cn_autosomes.tsv.gz` <br> `independent-specimens.*` | Combines mutation, copy number, and fusion data into an OncoPrint plot ([#6](https://github.com/AlexsLemonade/OpenPBTA-analysis/issues/6)); will need to be updated as all data types are refined | N/A

analyses/molecular-subtyping-SHH-tp53/README.md

@@ -1,8 +1,13 @@
-## _TP53_ mutation status in Medulloblastoma SHH subtype samples
+## Deprecated: _TP53_ mutation status in Medulloblastoma SHH subtype samples
 
 **Module Author:** Candace Savonen ([@cansavvy](https://www.github.com/cansavvy))
 
-The goal of this analysis is to further classify SHH subtype medulloblastoma samples into SHH, _TP53_-mutated and SHH, _TP53_-wildtype per [#247](https://github.com/AlexsLemonade/OpenPBTA-analysis/issues/247).
+The goal of this analysis was to further classify SHH subtype medulloblastoma samples into SHH, _TP53_-mutated and SHH, _TP53_-wildtype per [#247](https://github.com/AlexsLemonade/OpenPBTA-analysis/issues/247).
+
+**The notebook described below looked at any somatic _TP53_ mutations.
+According to the Medulloblastoma WHO 2016 book chapter linked on the issue, _TP53_ mutations are often found in exons 4 through 8 and are germline mutations about half the time.
+We do not have information regarding the presence or absence of _TP53_ germline mutations for this cohort.
+The mutation status table in `results` should not be used for subtyping.**
 
 We use `molecular_subtype` information from the harmonized clinical file (`pbta-histologies.tsv`) to restrict our analysis to samples classified as `SHH`.
 The medulloblastoma subtype classifier uses RNA-seq data, so we must identify WGS biospecimens that map to the same `sample_id`, if available.