get genotypes with nucleotides ?

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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get genotypes with nucleotides ? #45

Closed thierrygosselin closed 5 years ago

thierrygosselin commented 5 years ago

Is there a way to get (SeqArray::seqGetData) genotypes in the form of nucleotides, e.g. A/T similar to SeqVarTools::getGenotypeAlleles ? The last one is very slow for big VCFs. cheers Thierry

smgogarten commented 5 years ago

I might be able to speed up the implementation in SeqVarTools (no guarantees); I opened an issue here: https://github.com/smgogarten/SeqVarTools/issues/2

If Xiuwen has a better solution, I'd be happy to make use of it.

thierrygosselin commented 5 years ago

Awesome!