Closed antunderwood closed 5 years ago
Thanks to a personal communication from @simonrharris the answer to this is fairly obvious if I had thought about it 😳
Because my sequences were non-random there were split kmers with the same flanking sequence of 15 G's and either a central base of G or A in sample 1 and G or T in sample 2. Since this is reference free there is no way to align kmers in repeated sequences
If I make
ska fasta -o sample1 sample1.fas
ska fasta -o sample2 sample2.fas
ska distance sample1.skf sample2.skf -o sample1_vs_sample2
This produces a file sample1_vs_sample2.distances.tsv that rightly determines that there are 2 SNPs
In trying to understand split kmers produced from fasta files I produced 3 simple and very non-biologically relevant fasta files
ref.fas (a string of 160 Gs)
As expected this produced 1 split kmer as shown by the humanized summary
The 2nd fasta file (sample1) had just one polymorphism (G->A) at position 90
This file produced 31 split kmers as expected but the kmer that should have had an A as the middle base is reported with an N I think
The 3rd fasta file (sample2) had another one polymorphism (G->T) at the same position 90
Similar thing with the split kmer file
And when I calculated the distance between sample 1 and 2 using
ska distance sample1.skf sample2.skf -o sample1_vs_sample2
the output showed no SNPs