SeqArray reading problem with vcf from samtools

zhengxwen / SeqArray

Data management of large-scale whole-genome sequence variant calls (Development version only)

http://www.bioconductor.org/packages/SeqArray

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SeqArray reading problem with vcf from samtools #65

Closed thierrygosselin closed 3 years ago

thierrygosselin commented 3 years ago

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:

Error in SeqArray::seqGetData(gdsfile = my.gds, var.name = "$ref") : 
  The GDS node "$ref" does not exist.

Thanks for your help

thierrygosselin commented 3 years ago

Works on my end when I change the header of PL from Number to .