breast_alpelisib_2020 update

[yichaoS]

• check with author/PI if the customized patient ID could be changed to use the original MSKIMPACT patient ID, and add the customized ID into a separate column such as “OTHER_PATIENT_ID” or “INVESTIGATOR_ID”
• also check with author/PI if study ID could be changed to follow our convention.
• Change sample_id naming format to show them in the order of treatment time in mutation tab
• calculate VAF

[rmadupuri]

Checklist of tasks from todays call:

• [x] Update the study name to follow our convention. Breast Cancer (MSKCC, Nature Cancer 2020)
• [x] Also, change the description to our convention. use cfdna instead of ctdna for consistency.
• [x] Use DMP patient IDs. And shift the clinical trial patient IDs to PATIENT_DISPLAY_NAME attribute. Use the following pattern P001, P045 etc., instead of p1, p45..
• [x] Update the Sample Ids. change p1_post_cfdna to P001_cfDNA_04_Post to follow the order of treatment. tumor(01), pre(02), on(03) and post(04) in the mutation tab.
• [ ] calculate VAF for Genomic Evolution plot.
• [x] Add the sample type to tumor samples.
• [x] convert the PIK3CA pre treatment tumor/mutation to patient level.
• [x] Update the clinical attribute priorities. Exp design attributes first and Response related attributes later. The order should be treat Arm, treat resp, alp sch, alp dose, end thr, meas dis, tum seq plt, sample class, sam coll time, breast can subty, clin benefit, weeks on st, resist resp, off st reason, pik3ca.
• [ ] FGA and MC vs. FGA specific to tumor samples. update the names wrt to tumors.(is it possible?) or change the priorities to display them at the end.
• [ ] distinguish bet CT, CTD for pat and sample level. Make a pie chart for this? CT, CTD should be patient level (according to pedram the total count and freq should be pat related)