what program can do filter vcf file with below creteria? which program give me mean and SD of read depth?
i) SNPs and indels with overall quality less than 20; (ii) variants with very low or very high read depth. First we calculated the mean and standard deviation read depth for all the variants. We then set the minimum acceptable coverage as 10% of the mean and the maximum acceptable coverage as the mean read depth plus three times the standard deviation; (iii) variants with less than one forward or reverse alternative allele read; (iv) variants within 5 bp of each other; (v) SNPs within 5 bp of an indel; (vi) indels within 10 bp of each other.