I've sent over email a problematic VCF generated with samtools. Probably because the VCF format is not followed correctly with the headers, SeqArray doesn't seem to import properly, e.g. SeqArray::seqGetData(gdsfile = my.gds, var.name = "$ref") returns:
Error in SeqArray::seqGetData(gdsfile = my.gds, var.name = "$ref") :
The GDS node "$ref" does not exist.
Hi Xiuwen,
I've sent over email a problematic VCF generated with samtools. Probably because the VCF format is not followed correctly with the headers, SeqArray doesn't seem to import properly, e.g.
SeqArray::seqGetData(gdsfile = my.gds, var.name = "$ref")
returns:Thanks for your help