Closed gtonkinhill closed 5 years ago
Yeah that would be great! It would be very helpful for any within-host mixed sample analysis.
I've added the option to output allele counts during ska fastq and also ska humanise to output kmers in a human readable format (with the middle bases of each sample). You should be able to use the first column from that to find your allele frequencies in the allele count files.
SKA doesn't have that information at that stage, but I could output it from ska fastq and provide a way to look up allele frequencies based on a set of split kmers. Would that work?