SNPRelate for organelle genome (mitochondria or chloroplast)

zhengxwen / SNPRelate

R package: parallel computing toolset for relatedness and principal component analysis of SNP data (Development version only)

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

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SNPRelate for organelle genome (mitochondria or chloroplast) #93

Open ucabuk opened 2 years ago

ucabuk commented 2 years ago

Hi,

I am working on variant analysis of organelle genome but I could not make sure If I use my output files in SNPRelate for this purporse. Because method parameter in "snpgdsVCF2GDS_R" function is called as "biallelic_only". I am a bit confused. Do you have any recommendations to use SNPRelate for this purporse ? OR what kind of a way should I follow using SNPRelate ?

zhengxwen commented 2 years ago

Please use the SeqArray package instead.

ucabuk commented 2 years ago

Hi Xiuwen,

Thank you for your suggestion. I will try it.