This script merges VEP with SpliceAI info and generates SAIGE annotations according to BRaVa's guidelines. The required inputs for the annotations by VEP and SpliceAI are table format files (tab-delimited).
This script requires numpy and pandas to be installed in your Python environment.
python brava_create_annot.py -c <chromosome> -v <path_to_vep_table> -s <path_to_SpliceAI_table> -w <working_directory> --vep_snp_id_col <VEP SNP ID column> --vep_gene_col <VEP GENE ID column> --vep_lof_col <VEP LoF column> --vep_max_pop_col <VEP gnomAD_maxAF column> --vep_mane_select_col <VEP MANE SELECT column> --vep_revel_col <VEP REVEL column> --vep_cadd_phred_col <VEP CADD_PHRED column> --vep_consequence_col <VEP Consequence column>-c/--chr: Specify the chromosome to process. This is a required argument.-v/--vep: Specify the file path for the VEP annotation (tab-delimited). This is a required argument.-s/--spliceai: Specify the file path for the SpliceAI annotations. This is a required argument.-w/--work_dir: Specify the working directory. This is an optional argument, with the default being the current directory ('./').--vep_snp_id_col: Specify the SNP ID (chr:pos:ref:alt) column in the VEP table. This is a required argument.--vep_gene_col: Specify the GENE ID column in the VEP table. This is a required argument.--vep_lof_col: Specify the LoF column in the VEP table. This is a required argument.--vep_max_pop_col: Specify the gnomAD_maxAF column in the VEP table. This is a required argument.--vep_revel_col: Specify the REVEL column in the VEP table. This is a required argument.--vep_cadd_phred_col: Specify the CADD_PHRED column in the VEP table. This is a required argument.--vep_consequence_col: Specify the Consequence column in the VEP table. This is a required argument.
The script will generate the SAIGE annotation file for the given chromosome in the working directory. The output file name will follow the pattern brava_SAIGE_group_chr<chromosome>.txt.