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Calling Multi-allelic sites in pooled samples
Is GATK Unified genotyper able to call multi-allelic positions in a single pooled sample? Case is a pool of 13 samples, we use UG with ploidy set to 26. If I understand the supplementaries of the original publications correct, UG will never be able to call three alleles at a single position. in single sample calling. Or does this not hold for high ploidy analysis?
If needed, we can call multiple pools together, but this becomes computationally intensive.
In summary, we would like to call a 14xG,6xA,6xT call for example.
Also, how does UG take noise into account when genotyping (sequencing errors), when for example 3% of reads is aberrant at a position, this could correspond to ~ 1/26.
Thanks for any guidelines,