Unified Genotyper
Posted in Ask the GATK team | Last updated on 2013-02-06 21:31:28


Comments (3)

I am using Unified Genotyper to call variants from multiple samples. I have used the emit_all_confident_sites flag. The output vcf file occasionally has two entries for one position. It is always a monomorphic site and the depth between the two entries is quite different. Usually one entry has very high depth & when I return to the original bam file, the depth does not match. Any idea what I am missing here?


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