GATK validation with Sanger sequencing
1) Does GATK have a module that allows validation of SNP calls when Sanger reads are provided for the same individual for parts of the genome?
2) All False positive calls of GATK happen at variant sites. I.e., sites that are variant(0/1) in one individual are the sites that are incorrectly called as a SNP(0/1) in other individuals in which they are not variant(0/0).
Based on the parts of the genome that we sanger sequenced, as much as 5% of the SNP calls at "variant sites" was False positives. Does this number make sense? Or is my dataset or callset horribly wrong. Any information about the False positive rates is welcome.
(My dataset: ~10X average coverage, 50 Kb region Sanger sequenced)