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QUAL vs GQ in GATK
I am trying to do SNP analysis and using GATK's UnifiedGenotyper to call the SNP's. GATK gives me a vcf file in which I find there are both QUAL field and GQ field. As I understand, QUAL field indicates if there is a SNP at that particular site and GQ gives the confidence for that particular genotype. Am I right? If I want to do a pathway analysis which might be important to consider - QUAL or the GQ? Also if somebody could clarify how the FILTER field is determined, it will be great!
Thanks.
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