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Old 10-30-2015, 09:46 AM   #3
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Location: Washington, DC

Join Date: Sep 2011
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Originally Posted by Brian Bushnell View Post
I'm very confused. What are you trying to accomplish? And what organism are you working with? - and, does it have a reference genome?
My species does not have a reference genome. There is a draft genome of a closely related species that I am using as a starting point. I used GATK alternate reference maker to incorporate the differences in my sequence contigs (SNPs etc) into a new reference genome that incorporates the structure of the sister species with the SNPs from my species.

My end goal is two-fold:

1. Identify SNPs across a large number of individuals to look for population structuring and kinship between individuals with known and unknown pedigree data.

2. Identify highly heterozygous SNPs to create an array to perform SNP genotyping at 150 SNPs for more than 1500 individuals.

Hopefully this explains my questions more. Thanks for any thoughts.
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