Hi All,
I'm looking for the best method to do SNP genotyping on ~2000 loci for ~2000 individuals in a diploid plant species (600Mbp). We have a reference genome on the way (1000s of scaffolds still) and RAD tag pooled data has identified 1000s of potential SNPs several we have genotyped using KASPER.
Seems like this kind of genotyping is still not easy using NGS. Individual based (barcoded) RAD tag genotyping may be out of reach due to the workload in library prep required for 1000s of individuals. Plus there is the depth vs. coverage tradeoff because scoring diploid genotypes would require perhaps 15 depth per individual to reliably score hets.
SNP chips are one possibility - using SNPs identifying from RAD pools. What does this cost for non-model systems these days?
Would custom Open-Array Taq Man from AppliedBiosystems be an option? This one sounds exciting and I know that some people are trying this out in non-model systems. So I'm curious if anyone has experience with this method and what investment is required in terms of equipment? Is it comparable to SNP chip on a per sample cost?
Any advice on the subject is much appreciated!
Dave
I'm looking for the best method to do SNP genotyping on ~2000 loci for ~2000 individuals in a diploid plant species (600Mbp). We have a reference genome on the way (1000s of scaffolds still) and RAD tag pooled data has identified 1000s of potential SNPs several we have genotyped using KASPER.
Seems like this kind of genotyping is still not easy using NGS. Individual based (barcoded) RAD tag genotyping may be out of reach due to the workload in library prep required for 1000s of individuals. Plus there is the depth vs. coverage tradeoff because scoring diploid genotypes would require perhaps 15 depth per individual to reliably score hets.
SNP chips are one possibility - using SNPs identifying from RAD pools. What does this cost for non-model systems these days?
Would custom Open-Array Taq Man from AppliedBiosystems be an option? This one sounds exciting and I know that some people are trying this out in non-model systems. So I'm curious if anyone has experience with this method and what investment is required in terms of equipment? Is it comparable to SNP chip on a per sample cost?
Any advice on the subject is much appreciated!
Dave