Normal_melano_ucsf_2020

[stockschl]

updated PR for Tang et al., Nature 2020

Cancer studies updated in this pull request:

• a
• .

checks

For all pull requests:

• [ ] Passes validation

For a new study (in addition to above):

• [ ] Does study name and study ID follow our convention? e.g. Tumor_Type (Institue, Journal Year); brca_mskcc_2015
• [ ] is study meta data complete? e.g. pmid, group of PUBLIC
• [ ] were all samples profiled with WES/WGS? If not, is gene panel file curated?
• [ ] are oncotree codes of all samples curated; Cancer Type and Cancer Type Detailed needs to be added in addition to Oncotree Code
• [ ] clinical sample and patient data with meta files
• [ ] mutations data with meta files
• [ ] MAF is based on hg19
• [ ] MAF with 2 isoforms: uniprot and mskcc
• [ ] CNA data with meta files
• [ ] CNA segment data with meta files
• [ ] Expression data including z-scores with meta files
• [ ] Case-lists for all profiles.
• [ ] Manual checking (Niki or JJ): Triage or private Portal link here

[Rima-Waleed]

Hi @stockschl, thanks for updating the PR! Everything looks great but I noticed a couple of minor errors:

1. Study meta: SKIN is not a valid cancer type, can this be changed to 'skin'?

2. Sample file: The column (columns G, H) names (rows 1 & 2) in the sample file are mixed together and would need to be adjusted to match the attribute name.

3. Case list: This study needs a 'cases_all' and 'cases_sequenced' files. The case list file needs to be fixed, please see here.

4. MAF: A couple of data rows are missing the Hugo_Symbol and Variant_Classification (ex. row 129, 411, 412, 422...), can you verify that?

5. Gene panel matrix: The matrix file has some values (15) that are not genes- can you verify this?

Thank you!