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Can I persuade GATK to resolve 2 indels as 3 SNPs?

I have the following two haplotypes in my data:


GATK is (not incorrectly) resolving this as an insertion of T after position 1 and deletion of T at position 6. However, I would really like this to be resolved as 3 SNPs at positions 3 (G/T), 4 (A/G) and 6 (T/A). Is there some parameter I can change to get GATK to resolve things in this way?



  • SheilaSheila Broad InstituteMember, Broadie admin


    No, I am not aware of any parameters that will do what you are asking. Can you please post a screenshot of the artificial haplotypes created by HaplotypeCaller? You can view them in the bamout file. I am wondering if the 3 SNPs option is present in the artificial haplotypes as well as the 2 indels.


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