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Union of two VCF's in GATK

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  • Union of two VCF's in GATK

    Hi,

    I am using GATK in which I use their 'CombineVariants' to merge two VCF files which might have two different QUAL values. I see that if there are two records at a particular chromosome position, both of which has passed the quality filter in their respective files, then the merged file has a single record with the highest of the values in the QUAL field. My question is how do I get both QUAL values which are present in each file.
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