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?