Convert CADD annotations to VCF

cadd2vgf

#!/usr/bin/env python

#
# Converts the CADD format to VCF
#

import sys
import csv

print('''##fileformat=VCFv4.2
##INFO<ID=CADD_SCORE,Number=A,Type=Float,Description="CADD Score">
#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO''')

reader = csv.reader(sys.stdin, delimiter='\t')
writer = csv.writer(sys.stdout, delimiter='\t')

for row in reader:
    if row[0].startswith('#'):
        continue
    chrom, pos, ref, alt, cadd_score, cadd_phred = row
    writer.writerow([chrom, pos, '.', ref, alt, cadd_phred, '.', 'CADD_SCORE={}'.format(cadd_score)])