How to split multiallelic row to biallelic rows in variant annotation file(.vep.vcf)

Question

Input:

#CHROM  POallelic   REF     ALT     QUAL    FILTER  INFO    FORMAT  SAMPLE1
10      111     .       A       ACCA,TCGG       .       PASS    AC=4,2;AF=0.345,0.25;AN=8      GT:AD:DP:GQ:PL  0/1:2,15,31:30:99:2407,0,533,697,822,574

Expected output:

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  SAMPLE1
10      111     .       A       ACCA    .       PASS    AC=4;AF=0.345;AN=8;OLD_MULTIALLELIC=20:101:A/ACCA/TCGG GT:AD:DP:GQ:PL  0/1:2,15:30:99:2407,0,533
10      111     .       A       TCGG    .       PASS    AC=2;AF=0.25;AN=8;OLD_MULTIALLELIC=20:101:A/ACCA/TCGG  GT:AD:DP:GQ:PL  0/.:2,31:30:99:2407,697,574

Code: import os import sys

def main():
    
    PATH_Annotation_file='./XXXX.vep.vcf'
    PATH_output='./XXX.txt'
    
    parser_annotation_file = ParseAnnotationFile(PATH_Annotation_file, PATH_output)
    file = parser_annotation_file.extract_allele_information()  
    print(file)


class ParseAnnotationFile:
    def __init__(self, 
                path_Annotation_file,
                path_output):
        self.path_Annotation_file = path_Annotation_file
        self.path_output = path_output

        
    def extract_allele_information(self):
        path_Annotation_file = self.path_Annotation_file
        

        bool_start_variant = False
        
        with open(path_Annotation_file, "r") as vep_vcf:
            for line in vep_vcf:
                
                if "#CHROM" in line:
                    bool_start_variant = True
                    continue
                
                elif bool_start_variant:
                    list_variant = line.split('	')
                    
                    info = list_variant[7]
                    
                    list_info = info.split(';')
                    print(list_info[0][3:])  # Allele_Count
                    print(list_info[1][3:])  # Allele_Frequency
                    print(list_info[2][3:])  # Allele_Number
        

if __name__ == "__main__":
    main()

I'm trying to split multiallelic row to biallelic rows in variant annotation file(.vep.vcf). However, I don't have ideas to duplicate rows and write other materials in 'ALT' column, 'INFO column's AC,AF,AN' each row. Please let me know it if you have a good idea. Thank you!

How to split multiallelic row to biallelic rows in variant annotation file(.vep.vcf)

0 Answers