Skip to content

Generate de novo release #654

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

Merged
merged 33 commits into from
Mar 19, 2025
Merged

Generate de novo release #654

Show file tree
Hide file tree
Changes from 24 commits
Commits
Show all changes
33 commits
Select commit Hold shift + click to select a range
7812365
Generate de novo calls with new function
KoalaQin Jan 28, 2025
4b1355a
Add Julia's changes for dense MT and clean up
KoalaQin Jan 29, 2025
277e2fc
revert a comment
KoalaQin Jan 29, 2025
d3a6d3d
Apply suggestions from code review
KoalaQin Jan 30, 2025
da2af71
Address review comments
KoalaQin Jan 30, 2025
e157ed3
Merge branch 'qh/denovo' of https://github.com/broadinstitute/gnomad_…
KoalaQin Jan 30, 2025
dba9f98
Change to use new functions from gnomad_methods
KoalaQin Jan 31, 2025
73fd7da
import new function
KoalaQin Jan 31, 2025
7c8bc8b
Select entries and transmute colnames
KoalaQin Feb 3, 2025
d6fbcb4
Change the filter step
KoalaQin Feb 6, 2025
0966825
Modify comment about missing AD
KoalaQin Feb 10, 2025
af47133
Reflect gnomad_methods changes
KoalaQin Feb 12, 2025
db83d47
Add aggregate and annnotate function
KoalaQin Feb 18, 2025
79b5ae2
Clean up the aggregate function
KoalaQin Feb 21, 2025
aa66a8a
Clean up the functions
KoalaQin Feb 21, 2025
f3f67f3
Change docstring
KoalaQin Feb 21, 2025
d3a15dc
Address review comments
KoalaQin Feb 21, 2025
d793b96
remove postfix
KoalaQin Feb 21, 2025
bb179fd
Correct errors
KoalaQin Feb 21, 2025
fb279ed
Add mixed_site
KoalaQin Feb 21, 2025
8f5c4ff
Put coding_sequence_variant back
KoalaQin Feb 21, 2025
def7de5
Address review comments
KoalaQin Feb 24, 2025
dc07534
Fix bad operand for string
KoalaQin Mar 5, 2025
9257250
Change to add medium P>=0.9 to the high-quality
KoalaQin Mar 12, 2025
3b4d7b7
Change to high-quality
KoalaQin Mar 12, 2025
c18a209
Address review comments
KoalaQin Mar 12, 2025
75e6d4e
change to agg.take
KoalaQin Mar 13, 2025
bd61a27
add indentation
KoalaQin Mar 13, 2025
7058d59
Adjust docstring
KoalaQin Mar 17, 2025
6bd5796
Only getting high-quality
KoalaQin Mar 17, 2025
5e5662e
fix typo
KoalaQin Mar 17, 2025
302f53e
Update gnomad_qc/v4/create_release/create_de_novo_release.py
KoalaQin Mar 17, 2025
8de2196
Apply suggestions from code review
KoalaQin Mar 17, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
Loading