Hi,

I have list of VCFs ,when i tried to unlist them ,i got this error

> vcf <- do.call(rbind,vcfList)
Error in validObject(.Object) : invalid class "GRanges" object:
    'seqlevels(seqinfo(x))' and 'levels(seqnames(x))' are not
    identical
Calls: do.call ... .unlist_list_of_GenomicRanges -> new ->
    initialize -> initialize -> validObject
In addition: There were 23 warnings (use warnings() to see them)
Execution halted

Any idea?

Thank you 

Hi,

Looks like a problem rbind'ing the rowData. Try lapply over the 'vcfList', extract rowData and call seqinfo on each rowData. Assuming you don't have too many VCFs this visual inspection should show some discrepancy (ie, dissimilarity) in the GRanges.

Valerie