Dear all, I would appreciate having a piece of advice :

shall we use the VariantAnnotation package, how shall I filter a VCF file in order to exclude the GERMLINE and TUMOR samples that have a GENOTYPE of "./".

for example, if we aim to see the GENOTYPES in the vcf file, we receive the following messages :

> geno(vcf)$GT[,"TUMOR"]
Error in geno(vcf)$GT[, "TUMOR"] : subscript out of bounds
> geno(vcf)$GT[,"NORMAL"]
Error in geno(vcf)$GT[, "NORMAL"] : subscript out of bounds

thank you !

You can use filterVcf to remove rows from a vcf file that meet certain criteria. (The function does not filter by sample/column.)

From the ?filterVcf man page:

There are up to two passes. In the first pass, unparsed lines are passed to \code{prefilters} for filtering, e.g., searching for a fixed character string. In the second pass lines successfully passing \code{prefilters} are parsed into \code{VCF} instances and made available for further filtering. One or both of \code{prefilter} and \code{filter} can be present.

So the 'prefilter' would use grep on each line of the vcf file (similar to "lowCoverageExomeSNP" on the man page) and the 'filter' would use VCF class extractors to get at the data persome some sort of matching (similar to "VTisSNP" on the man page).