In step 1b, it is said "We can use the helper function select_mamba_loci() to combine the pruned and clumped variants, removing any pruned SNPs within 500kb of a clumped SNP." However, in the subsequent example script, it looks that only clumped SNPs are used to filter SNPs in the locus without taking account of pruned variants. If so, how can we incorporate the pruned variants in the function select_mamba_loci()?
Thanks in advance!
In step 1b, it is said "We can use the helper function select_mamba_loci() to combine the pruned and clumped variants, removing any pruned SNPs within 500kb of a clumped SNP." However, in the subsequent example script, it looks that only clumped SNPs are used to filter SNPs in the locus without taking account of pruned variants. If so, how can we incorporate the pruned variants in the function select_mamba_loci()?
Thanks in advance!