For a test vcf of the following format, the script will output the frequency of the reference allele.
##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 20389_S5.bam chr1 11205058 rs1057079 T A 100 PASS DP=12;BC=105,96,0,1;cosmic=1|COSM4142146;EVS=0.545902|115|6503;GMAF=C|0.4525;AA=C;AF1000G=0.547524;phyloP=0.078;CSQT=1|MTOR|NM_004958.3|synonymous_variant,1|MTOR-AS1|NR_046600.1|intron_variant&non_coding_transcript_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:43:0,12:12:1.000:20:-100.0000:0.0000 chr1 11253467 rs28991008 A G 100 PASS DP=90;BC=130,0,0,86;GMAF=A|0.02516;AA=C;AF1000G=0.02516;phyloP=0.241;CSQT=1|MTOR|NM_004958.3|intron_variant,1|ANGPTL7|NM_021146.3|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:100:38,52:90:0.578:20:-100.0000:0.0000 chr1 11288758 rs1064261 A G 100 PASS DP=93;BC=122,0,0,111;cosmic=1|COSM4142152;EVS=0.617561|95|6503;GMAF=G|0.2995;AA=A;AF1000G=0.700479;phyloP=-0.406;CSQT=1|MTOR|NM_004958.3|synonymous_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:100:0,93:93:1.000:20:-100.0000:0.0106 chr1 11297762 rs7524202 A G 100 PASS DP=48;BC=124,0,0,110;GMAF=T|0.2991;AA=C;AF1000G=0.700879;phyloP=-0.016;CSQT=1|MTOR|NM_004958.3|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:100:0,48:48:1.000:20:-100.0000:0.0204