genotypes have been called in haploid mode, they don't have a phase

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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genotypes have been called in haploid mode, they don't have a phase #52

Closed JiruHan closed 5 years ago

JiruHan commented 5 years ago

Hi there, I have a problem using the function getGenotype, when I run getGenotype(gds), it has an errot: Error in seqApply(gdsobj, c(geno = "genotype", phase = "phase"), function(x) { : The GDS node "phase/data" does not exist. I don't know how to solve this problem, could you please help me? Thanks in advance!

Cheers, Jiru

smgogarten commented 5 years ago

Try seqGetData(gds, "genotype"). Opened as issue in SeqVarTools: https://github.com/smgogarten/SeqVarTools/issues/3

smgogarten commented 5 years ago

Fixed in SeqVarTools https://github.com/smgogarten/SeqVarTools/commit/390dfa26d10c22167393a93b4b29e16f86f58dd4