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Genotyping a substitution using the HaplotypeCaller
I have the following substitution that I am trying to genotype in a deep coverage (>1000x) dataset:
4 2558307 GCTGATGTGGGG GAGCTACTCAA
I've aligned it using very relaxed BWA parameters and am now getting it correctly with the Haplotype caller, however it is currently genotyped as multiple indel/SNP events:
4 2558307 G GAGCTA
4 2558310 G C
4 2558311 ATGTGGG A
4 2558318 G A
Filling the blanks between the events above using the reference sequence gives exactly the substitution I am looking for however I'd like to genotype this as one substitution event. I've tried playing with the following options but I never got any results using them:
--fullHaplotype --genotypeFullActiveRegion --activeRegionIn 4:2558307-2558318 --activeRegionOut substitution.out
I am not sure if what I'm trying to do is feasible but would appreciate any advice.
Thanks a lot!