BioMuta ReadTheDocs Notes

[mariacuria]

Issue in Step 1: Download - TCGA

1. Gain All Access Requirements (there is a typo in "Requiremenets")

Contact Dr. Fabian Seidle and ask for access to the ISB-CGC Big Query repository

• Not clear how to contact
• Is he still the contact person for that?

[mariacuria]

Issue in Step 1: Download - TCGA

ETA: @rajamazumder already has access and shared the keys with me

1. Gain All Access Requirements

Gain access to dbGaP data

• Apply for access to controlled data at this website
• Since I am not a senior permanent employee, I am not eligible to apply.

This is who can apply for access to dbGaP Data Download:

• Senior Investigators
  • Extramural Investigators must be permanent employees of their institution at a level equivalent to a tenure-track professor or senior scientist with responsibilities that most likely include laboratory administration and oversight. Laboratory staff and trainees such as graduate students and postdoctoral fellows are not permitted to submit project requests.
• NIH Investigators
  • NIH Intramural Investigators must be tenure-track investigators, senior investigators, senior scientists, senior clinicians, or staff scientists.
  • NIH extramural scientific staff must have administrative responsibility for the data; have substantial research involvement in the award that generated the data; or need access to carry out research unrelated to their portfolio management responsibilities.

[mariacuria]

Issue in Step 1: Download - TCGA

1. Gain All Access Requirements

For further information see the ISB-CGC documentation on gaining access

• Dead link

[mariacuria]

Comment for Step 1: Download - CIVIC

ETA: Newer VCF files are slightly different in terms of columns.

A VCF for the monthly relaease of accepted variants was downloaded from: https://civicdb.org/releases/main Downloaded File: 01-Aug-2022-civic_accepted.vcf

• The latest Data Release is from 01-Sep-2024
• Conclusion: CIVIC is up to date.

[mariacuria]

Issue in Step 1: Download - COSMIC

• Download links not provided.

[mariacuria]

Issue in Step 1: Download - ICGC

ETA: We won't include ICGC.

• The ICGC Data Portal was retired in June 2024.

[mariacuria]

@seankim658 @jeet-vora

1. I'm still learning the ticket system. Am I doing it correctly?
2. I will need access to these datasets to continue walking through the pipeline. I can already do CIVIC because it's up-to-date and available.

[jeet-vora]

@mariacuria I would suggest to create a BioMuta Project board and create separate tickets for each resource and other tickets for other tasks. Do not club everything in one ticket.

subs tasks under one main task can be group like below using the Task List option. You can also create labels such as TCGA or pipeline or access etc You can also link tickets. Spend 30 mins or so to on YT to see how to use GitHub for tickets/issues

Main Task

• [ ] 1
• [ ] 2
• [ ] 3