Repository for code and extra materials for the Advanced Clinical Bioinformatics (BIOL68412) Assignment.
- Cardiac_Transcripts.bed
- BED file of genes and transcripts used
- Cardiac_Targets.bed
- BED file of targets used for analysis. Created using HyperDesign, all exon targets have a 15bp overhang
- Filter_Annotation.py
- Python script to filter the VEP output
- Python3
- openpyxl module installed
- Download VEP output in txt format
- Ensure RefSeq transcripts were used in VEP
- Ensure gnomAD allele frequencies were included
- Place VEP txt output in the same location as Filter_Annotation.py and Cardiac_Transcripts.bed
- Run the script using the -f flag to specify the input file name e.g:
- python3 Filter_Annotation.py -f VEP_output.txt
- The output file will be named based on the input file e.g:
- If the input filename was VEP_output.txt the filtered annotation file will be named VEP_output_FILTERED.xlsx