Collection of random scripts with no other home!
A python script to produce metrics on CNV calls from a VEP annotated VCF file. This script utilises the pyvariantfilter package to parse the VCF and matplotlib for plots.
A python script to filter the SpliceAI VCF file for genome build 38. Includes bash script for submitting this as a job on a SLURM scheduler.
A python script to take the output from CoverageCalculatorPy when split at exon level and produce average for each gene.
A python script to take a JSON file supplied by GOSH containing variant information and convert this to a csv file format containing just the key information on variant location, ref/alt allele, type and subtype.
A python script to query the PanelApp API for genes and to then parse the information to retrieve information on panels where the genes are reviewed as green.
A python script to get all patient and research variant for a given gene from decipher. Has it's own conda environment yml with necessary packages.
A python script to take an output from dbCAN and use this to predict PULs based on 15 genes up and downstream of a key class of GHs.