filtering large vcf. GQ and DP

Question

[kazakkaty]

hi everyone, i'm new in bioinformatics, i have a big VCF file, i get dp from there using dp = extract.gt (vcf, element = 'DP', as.numeric = TRUE) dpp = apply (dp, 2, sum) and I build a plot barplot (sort (dpp), las = 3, main = "DP", col = 1:12), I need to take averages from this graph and do a GQ analysis on them, how can I do that?

Answer 1

[Pierre Lindenbaum]

use bctools stats followed by plot-vcfstats https://samtools.github.io/bcftools/bcftools.html#plot-vcfstats