Is there a way to identify mixed samples based on SNPs?
Example input (table of genotypes for multiple samples):
| | sample1 | sample2 | sample3 | |------|---------|---------|---------| | rs1 | AA | BB | AB | | rs2 | AA | BB | AB | | rs3 | AA | BB | AB | | rs4 | AA | BB | AB |
Desired output: Sample relationships/distances. In this example, sample1 and sample2 are distinct, but sample3 is likely a mix of two (biological or technical).
Based on this simple example, the calculation seems doable, but maybe it's impossible in more complex realistic scenarios.
There is a nice tool peddy that does something conceptually similar, but it expects pedigree information as well as genotype frequencies for both the input samples and population.