SNPhylo Error Help: there is no SNP and Na/NaN arguement

Question

[N Smith]

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?

Answer 1

[Varvara]

I have a similar problem and for me, autosome.only=F has worked. Can you show the whole code that you uploaded?