Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

convert legacy data to masked GRCh38 #479

Open
4 of 10 tasks
marc-sturm opened this issue Aug 29, 2023 · 1 comment
Open
4 of 10 tasks

convert legacy data to masked GRCh38 #479

marc-sturm opened this issue Aug 29, 2023 · 1 comment
Assignees
@marc-sturm

Comments

@marc-sturm
Copy link
Member

marc-sturm commented Aug 29, 2023 •
edited
Loading

Todo:

  • convert BAMs of legacy samples to CRAM for diagnostics (WGS and WES) when GRCh38 with false duplications masked was used
  • correct for GRCh38 with false duplications not masked
  • re-create coverage profiles for CNV calling
  • delete BAMs

Pakreatitis control samples used by Andreas:

  • convert BAMs of legacy samples to CRAM when GRCh38 with false duplications masked was used
  • correct for GRCh38 with false duplications not masked
  • re-create coverage profiles for CNV calling
  • delete BAMs (when Andreashas published the pancreatitis data)

Finally:

  • run check_integrity script
  • perform variant calling on medically relevant genes (KCNE1, CBS, SIK1, PRODH) for samples where VC was not done on these genes. If report config exists, update report config for samples with causal variants, e.g. DX203954_02 - chr21:34449622-34449622 ->A
@marc-sturm marc-sturm self-assigned this Aug 30, 2023
@marc-sturm
Copy link
Member Author

marc-sturm commented Sep 15, 2023 •
edited
Loading

Implemented tool to fix BAMs that were mapped with a hg38 genome without masked false duplications: https://github.com/imgag/megSAP/blob/master/src/Tools/bam_fix_unmasked_duplications.php

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees

@marc-sturm marc-sturm

Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
1 participant
@marc-sturm