I have performed variant calling using the Platypus tool but cannot find allele frequency (AF) in the output file. I am trying to read the vcf file in VariantAnnotation and vcfR packages and want to calculate AF and add it into the INFO field of the VCF file. Please guide me how to calculate AF from my VCF file.
Find the info and geno field of vcf file,
rowRanges(vcf):
GRanges with 5 metadata columns: paramRangeID, REF, ALT, QUAL, FILTER
info(vcf):
DFrame with 25 columns: FR, MMLQ, TCR, HP, WE, Source, FS, WS, PP, TR, NF, TCF, NR, TC, END, MGOF, SbPval, START, ReadPosRankSum, MQ, QD, SC,...
info(header(vcf)):
Number Type Description
FR . Float Estimated population frequency of variant
MMLQ 1 Float Median minimum base quality for bases around variant
TCR 1 Integer Total reverse strand coverage at this locus
HP 1 Integer Homopolymer run length around variant locus
WE 1 Integer End position of calling window
Source . String Was this variant suggested by Playtypus, Assembler, or from a VCF?
FS . Float Fisher's exact test for strand bias (Phred scale)
WS 1 Integer Starting position of calling window
PP . Float Posterior probability (phred scaled) that this variant segregates
TR . Integer Total number of reads containing this variant
NF . Integer Total number of forward reads containing this variant
TCF 1 Integer Total forward strand coverage at this locus
NR . Integer Total number of reverse reads containing this variant
TC 1 Integer Total coverage at this locus
END . Integer End position of reference call block
MGOF . Integer Worst goodness-of-fit value reported across all samples
SbPval . Float Binomial P-value for strand bias test
START . Integer Start position of reference call block
ReadPosRankSum . Float Mann-Whitney Rank sum test for difference between in positions of variants in reads from ref and alt
MQ . Float Root mean square of mapping qualities of reads at the variant position
QD 1 Float Variant-quality/read-depth for this variant
SC 1 String Genomic sequence 10 bases either side of variant position
BRF 1 Float Fraction of reads around this variant that failed filters
HapScore . Integer Haplotype score measuring the number of haplotypes the variant is segregating into in a window
Size . Integer Size of reference call block
geno(vcf):
SimpleList of length 6: GT, GQ, GOF, NR, GL, NV
geno(header(vcf)):
Number Type Description
GT 1 String Unphased genotypes
GQ . Integer Genotype quality as phred score
GOF . Float Goodness of fit value
NR . Integer Number of reads covering variant location in this sample
GL . Float Genotype log10-likelihoods for AA,AB and BB genotypes, where A = ref and B = variant. Only applicable for bi-allelic sites
NV . Integer Number of reads containing variant in this sample
