This is the first time I used Variant Effect Predictor (VEP) and would like to use it to annotate the VCF files I got from WES data. I tried to set up some filters to include only the mutations with mutant allele frequency higher than 0.2 (Number of mutations/Total number of counts > 0.2).
This is the code I used:
./vep --cache --offline --symbol --coding_only \ --freq_freq 0.2 --freq_gt_lt gt --freq_filter include \ -i input.vcf -o output.txt
I checked the results by loading the bam files on IGV. However, I found that so far almost all the mutations in the results had allele frequency < 0.2. For example:
Total counts: 118 A: 0 C: 0 G: 102 (86%, 86+, 16-) T: 16 (14%, 16+, 0-) N: 0
The G -> T mutation has only 0.14.
Does anyone have experience in using VEP? The way I used it may be incorrect and could you point out what I am missing here? Thank you.