What method would you use to genotype SNPs in low quality samples?

Question

What method would you use to genotype SNPs in low quality samples? I ideally want to genotype hundreds of SNPs in hundreds of scat samples (very low amount of target DNA, potentially degraded and highly contaminated by other DNA).

Answer 1

You need to make sure you have high quality and specific primers for your PCR steps as your initial starting point.

Next Generation Sequencing can read low quality samples or smaller number of replicates better than some other methods.