The AF value VarDict calculate cannot match with IGV result.

[GA-1101]

Hi,

I recently found that the AF in vcf file VarDict called cannot match with IGV browser.

IGV shows that in Chr9:5073770 the mutation G > T has AF 5% (0.05):

but VarDict show this position just has AF 0.005, because I set threshold of AF is 0.01 so it cannot PASS the FILTER. I use -p to show its information:

My script is here:

vardict -G <hg19.fasta> -f 0.01 -N <sample_name> -b <bam_file> -c 1 -S 2 -E 3 -g 4 target_interval.bed | VarDictJava/VarDict/teststrandbias.R | VarDictJava/VarDict/var2vcf_valid.pl -N <sample_name> -E -f 0.01 > vars_VD.vcf