SNPhylo Error Help: there is no SNP and Na/NaN arguement
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4.8 years ago
N Smith ▴ 10

Hi All,

I'm trying to run snphylo on a VCF file. However, i keep getting the error

Removing 2120285 non-autosomal SNPs Error in snpgdsLDpruning(genofile, ld.threshold = ld.threshold, maf = maf.threshold, : There is no SNP! Execution halted

I added the line "-autosome.only=FALSE" and got a new error:

SNP pruning based on LD: Sliding window: 500000 basepairs, Inf SNPs |LD| threshold: 0.1 Error in opt$autosome.start:opt$autosome.end : NA/NaN argument Calls: snpgdsLDpruning -> %in% -> match Execution halted

How do I fix?

snphylo phylogenetic tree VCF • 1.8k views
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