I am currently trying to compare the alignment performance between vg and BWA-Mem. However, what I have found is not what I expected, vg does more or less the same as BWA in terms of number of mapped reads and number of correctly mapped reads. For inputs I have a VCF of ~1000 samples, a linear reference FASTA, and a VCF of a sample not in the large VCF. I have followed the workflows outlined in the wiki for construction, indexing, simulation and mapping.
The script map-sim seems to do what I am trying to achieve, and I have tried to emulate the workflow laid out in the script, but some parts have my confused. I am most interested in the simulation part of the script, particularly how the sim-base, sim-ref, and hap-base graphs are constructed.
Thanks in advance,