I am testing discoSNP++ on my data and I have some questions.
My data is composed of NGS Illumina paired-reads for three species of the legume genus Stylosanthes. Two species are supposed to be diploid parents of the third allotetraploid species. I was able to run discoSNP++ for all three samples, but I am not sure how can I compare the results between them. Is there possible to use vcf-compare to see shared and unique SNPs among all samples? Or can I just compare overall amount of SNPs found. If I use a set of contigs obtained from a de novo assembly of the allotetraploid and use this as reference for the mapping all samples, can I then compare unique and shared SNPs? For me it would be ideal to find shared and unique SNPs to support the allopolyploid origin of this species and further supports the two diploid as its parents.
Thanks in advance, André