Release notes
Version v1.4.0
- Add standardization of the new
cnv_sv
-file from Dragen - Remove the cnvLength filter from the
cnv
-file from Dragen - Refactor 'merge'-standardization:
merge
will now post-process the output of svdb merging.header
will just sort the VCF header as the header order is destroyed by many tools.ella
will introduce an ELLA compatible variant format
Version v1.3.0
- Introduce better functionality for making custom filters
- Changes to utils
- Allow the "search" relation to filters for doing regex search. Primarily meant for crude searching in the CSQ from VEP. Splitting on
,
and and require regex to match all parts. - Changes to
sv_postprocessing
allow checking for existence of INFO-fields and setting filter exceptions.
Version v1.2.0
- Introduce more flexible filtering definitions
- Changes to standardization
- Ensure minimal starting position is base 1
- Add
CN
from Canvas to theFORMAT
field when Canvas is merged with Manta
Version v1.1.0
- Rescue ACMG_class 4,5 and add ACMG_class column to TSV output
Version v1.0.0
Changes
Breaking change
- Removes the
--print
-argument from the Python scripts
New features
- Directly installs runnable scripts
sv_standardizer
sv_postprocessing
sv_wgs_filtering
- Moves parsing and formatting of VCFs into
src/sv_utils.py
- Remove non-variants (
DRAGEN:REF
) - Add INFO fields
canvasSM
,canvasPE
,canvasBC
to back up FORMAT fieldsSM
,PE
,BC
. Useful for merging.
Version v0.9.0
Version v0.9.0
of this repository was never released, but is a collection of the Python scripts hardcoded in the following repositories
svtools@v0.1.2
anno-targets@74a1b0f8a4f7045b8e8a628d059c2c0927e558d3