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Incosistent genotype results ?
I have ran UnifiedGenotyper (using GATK 3.4) in my set of 16 samples (all sequenced to high coverage ~ 80 X). But, I get weird genotype calls across samples. For e.g.
sample 1 : 0/1:83,30:114:13:13,0,2806 and sample 2: 0/0:70,27:97:43:0,43,2337
As you see, I have 27 out of 97 reads supporting variant allele in sample 2, but it is still called 0/0. I have about similar number of reads supporting variant allele in sample 1 (30 out of 114), but is called 0/1. Looking into IGV plot shows both these samples have enough support to be called heterozygous. Why do these differences appear ?