Hello

I made vranges object from my VCF file usingreadVcfAsVRanges. There are 37974 variants in the VCF file and in vranges there are 14682016 ranges. Can someone please explain this difference?

I guess that if a variant is in more than one sample then there will be more than one range for that variant in vranges object but even then there are too many number of ranges.

Regards

The data are expanded (replicated into rows) by the number of ALT values as well as the samples which may explain the difference. Reading in a small subset with a 'param' would allow you to inspect manually to see what's going on, e.g.,

param <- ScanVcfParam(which=GRanges("chr6", IRanges(5000, 6000)))

readVcfAsVRanges(myfile, param=param)

Valerie