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max_alt_alleles in UnifiedGenotyper

mike_boursnellmike_boursnell Posts: 72Member

If you are using UnifiedGenotyper to call Indels, and you are looking at an Indel which is hard to sequence (say 9 Ts versus 10 Ts) the sequencing may generate more different Indel alleles than there really are. What is the best way to deal with this situation if you actually only want one alt allele called? If you limit max_alt_alleles to 2, what does the software do?

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