Working with VCFs in Bioconductor

library(VariantAnnotation) vcf <- readVcf("GHS025_D1EH2ACXX_ATCACG_L001_R1.fastq.gz.dedupe.reorder.rg.recal.realign.snpeff.vcf", "hg19") # reduce the set to those not present in the unaffected, for each family # so not in GHS026, and in GHS025 and GHS027 # so not in GHS031, and in GHS015 and GHS008 # so not in GHS034, and in GHS036 and GHS033