v0.4.3

This release introduces some fixes and optimizations in the variant tagging systems.

This also resolves a bug affecting the extraction of custom CSQ columns (--csq_column argument). Column names are now normalized to uppercase when loading them, and the column names requested by the user are also converted to uppercase to ensure consistency. This ensures the values from the CSQ field are always extracted as intended.

Grab the pre-compiled executable to move to this release.

v0.4

This release introduces some new features.

• a new, more flexible scoring/tagging system. When creating TSV or rare var outputs, it is now possible to add a specific tag to an impact based on criteria evaluated on INFO fields and CSQ-block fields. One can also configure a scoring schema evaluated on INFO fields and CSQ-block fields and add a counter suffix that counts how many criteria are met.
• new aliasing feature. When creating TSV or rarevar outputs, one can set aliases for a group of variants. For example, set a single alias for all loss-of-function impacts
• some arguments have been renamed like the JSON config file is now -j, --var_tagging_json
• any field from INFO or CSQ-block can now be added as a column in the TSV output format.

Grab the binary to use this new release.

v0.3

This release mainly improves the scores logic used when generating regenie rare variants files.

• user can now use also criteria based on INFO flags in the score JSON
• all numeric values are now internally evaluated as Float to avoid wrong evaluation when setting an integer value threshold for a float INFO annotation

There are also minor improvements in the setlist creation logic and a better explanation of the filtering cascade in the README file.

Just grab the executable from the release or compile it locally.

v0.2

This new release introduces a new output format to generate files needed to perform rare variants association tests using regenie.

• new rarevar_set output format. This output format generates 2 output files: the first file (.annot) contains variants impact annotations (variant id, gene id, impact), while the second file (.setlist) contains the list of variants associated with each gene (gene id, chrom, position, variant id list).
• new --scores argument to refine impact annotations based on values in the INFO field. You can pass a JSON file to the --scores option to configure value thresholds to be applied for a specific impact and the variant annotation for that impact will reflect the number of scores thresholds that are passed (like missense-1, missense-2).

You can grab the new executable from this release.

v0.1.1

This version uses a better argument parsing and has better help usage message. Also logging during execution is improved. Few fixes in the code to improve speed. It can now process ~100k variants per second in the simplest scenario using only --most_severe filter.

v0.1.0

First public release. It works fine on annotations from snpEff, VEP and bcftools csq.

Grab the pre-compiled binaries and enjoy!