Hi,

I noticed that when I use VariantAnnotation::writeVcf() on a vcf file it will fill the ID column with a string that is the combination of chromosome, position, ref and alt allele. This happens even though the vcf file that I read in using VariantAnnotation::readVcf() had no values in the ID column. 

Is there a way to suppress these values in the VariantAnnotation::writeVcf output? In other words, I don't want the ID column to be filled with some identifier that is constructed in the final VCF output file.

Thanks,

Hi,

The ID values become the row names on the GRanges in rowRanges(vcf). As you saw, if IDs are missing, the default behavior is to use CHROM:POS_REF/ALT. To turn this off use 'row.names = FALSE'. I've updated the docs in devel to clarify this.

readVcf(myfile, "genome", row.names=FALSE)

Valerie