Releases: eastgenomics/eggd_generate_variant_workbook
Releases · eastgenomics/eggd_generate_variant_workbook
v2.0.3
- Fixed issue with long urls exceeding excel string length (see #92)
- Fixed issue with truncated values in hyperlinked cells (see #94)
- Changed app name to eggd_generate_variant_workbook due to permission errors with previously built app
v2.0.2
Bug fixes
- Bug fix for missing lines in ACMG report template
v2.0.1
Bug fixes
- Bug fix to correctly cast CHROM values to str before calling
.replace()
when mapping to NC values in vcf().make_hyperlinks()
v2.0.0
Summary
Rewrite of previous vcf2xls app to handle generating Excel workbooks from VCF(s) annotated with VEP.
Code structure:
generate_workbook.py
:
main()
calls functions to process vcfs (reading, filtering, formatting etc.) then writing to file
vcf.py
:
- main functions for doing all the VCF operations
process()
contains the main logic for calling all other methods
columns.py
:
- functions for splitting
INFO
and FORMAT
/ SAMPLE
fields from VCF to separate columns by fields
filters.py
:
- functions for handling running bcftools filter and modifying incorrect field types in VCF header
excel.py
:
- functions for writing to, formatting and verifying output Excel file
- unit tests written to cover core functionality of methods that modify data
v1.7.0
Changes
- Use raw vcf to get the single workflow id used
- Removal of
GEMINI_AF
from reports
v1.6.3
Changes
- Remove checking of variant position during the vcf integrity check
- Remove "syncing" attempt when comparing vcfs in vcf integrity check
v1.6.2
Bug fixes
- Vcf annotator switches alts around in multi allelic variants. This causes vcf integrity to fail --> use sets to compare alts between annotated vcf and sentieon vcf
v1.6.1
Vcf2xls changes
- Now highlights red variants only when all considered frequencies (i.e. not gemini) are below the rare variant threshold
v1.6.0
App changes:
- New input to app: annotations
Vcf2xls changes:
- remove esp, 1kg, exac AF in vcf2xls
- use annotation input to add custom annotation in the report
v1.5.2
Changes
Bug fixes:
- Pattern matching works when checking if sample is in the manifest
- vcf integrity check fix when the sliced vcf is empty