A batch program for calling filter SNVs from pileup files to Variant Call Format (VCF) files.
start the program by running the following command:
python3 snv_caller.py -pf <path to the pileup file> -o <output directory>
-md --min_depth <Minimum depth to call a variant | defult: 10>
-mbq --min_base_qual <Minimum quality to call a variant | default: 20>
-mac --min_alt_count <Minimum count for alternative base allele | default: 4>
-maf --min_alt_freq <Minimum alternative frequency to call a variant | default: 0.2>
-a --annotate <Annotate the the SNV's with effect prediction information | default: False>
The annotation is done via VEP REST API from the Ensemble genome browser. (Peter W Harrison et al. Ensembl 2024 Nucleic Acids Res. 2024, 52(D1):D891–D899 PMID: 37953337 10.1093/nar/gkad1049)