The new update to the annotation pipeline includes all annotation tools used for the published version of deeprvat, as well as all processing steps needed to create ready-to-run annotation data for the published deeprvat version.
Updates since last push:
inclusion of AlphaMissense annotations as plugin in VEP
changed DAG in order to optimize parallelisation
Allele Frequency, MAF and AF_MB calculated from genotype file
pipeline includes filtering step for variants based on distance to the nearest exon
selection of required columns for deeprvat as well as renaming of columns to fit required input is now performed
abSplice pipeline is now integrated into the DAG
spliceAI scores are aggregated to spliceAI_delta_sores
Testing
since the annotation tools rely on pre-scored data, automatic tests via GitHub actions is not completely possible
the annotation pipeline was instead tested locally using example data
What
The new update to the annotation pipeline includes all annotation tools used for the published version of deeprvat, as well as all processing steps needed to create ready-to-run annotation data for the published deeprvat version.
Updates since last push:
Testing