Handle variants with consequence type 'stop_retained' as synonymous variants.

connor-lab / ncov2019-artic-nf

A Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics), with a focus on ncov2019

GNU Affero General Public License v3.0

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Handle variants with consequence type 'stop_retained' as synonymous variants. #91

Closed dfornika closed 3 years ago

dfornika commented 3 years ago

Fixes #90

Check for both synonymous and stop_retained consequence types in type_vcf.py. Handle both as synonymous variants.