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

• Conversion to app

Bug fixes:

• Pattern matching works when checking if sample is in the manifest
• vcf integrity check fix when the sliced vcf is empty