It depends what you mean by SNP data. Are the SNPs genotyped using a platform that targets pre-defined loci with minor allele frequency exceeding some threshold (for example, Illumina Beadchip)? In that case, BPP cannot be used because the non-variable sites (which are informative for BPP as well) are missing.
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To follow up on this question, can we use it for RAD-seq type data where we have 100bp fragments sequenced? (i.e. both SNPs and the non-variable sites). Why does it need the non-variable sites?
Thanks!
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Is it possible to use SNP data with BPP?
It depends what you mean by SNP data. Are the SNPs genotyped using a platform that targets pre-defined loci with minor allele frequency exceeding some threshold (for example, Illumina Beadchip)? In that case, BPP cannot be used because the non-variable sites (which are informative for BPP as well) are missing.
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To follow up on this question, can we use it for RAD-seq type data where we have 100bp fragments sequenced? (i.e. both SNPs and the non-variable sites). Why does it need the non-variable sites?
Thanks!