skills/bioskills/bio-liquid-biopsy-ctdna-mutation-detection/scripts/detect_ctdna_mutations.py

• call_variants_vardict · function · L21-L37 — def call_variants_vardict(bam_file, reference, bed_file, output_vcf, min_vaf=0.005)
• parse_vcf_variants · function · L40-L53 — def parse_vcf_variants(vcf_file)
• flag_chip_variants · function · L56-L64 — def flag_chip_variants(variants_df, chip_genes=None)
• track_known_variants · function · L67-L90 — def track_known_variants(bam_file, variants)