I am conducting work on a haploid data set and used seqVCF2GDS() to read in the original VCF for the set. After some assessment and filtering, I ran into an issue with seqGDS2VCF(), where it seems to require the "phase/data" node, missing in the GDS file generated from seqVCF2GDS().
Since the samples are haploid and no phasing information is available in the source VCF I can see why the function does not incorporate one, but if that is the case could seqGDS2VCF() have the ploidy as an optional flag so it knows to exclude the missing "phase/data" node?
I am conducting work on a haploid data set and used seqVCF2GDS() to read in the original VCF for the set. After some assessment and filtering, I ran into an issue with seqGDS2VCF(), where it seems to require the "phase/data" node, missing in the GDS file generated from seqVCF2GDS().
Since the samples are haploid and no phasing information is available in the source VCF I can see why the function does not incorporate one, but if that is the case could seqGDS2VCF() have the ploidy as an optional flag so it knows to exclude the missing "phase/data" node?