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how to increase our call confidence
Our call variants analysis, has more far more variants than we expect, including some low-call-confidences and non-coding variants on whole exome. Is there any suggestion on how to increase our call confidence and decrease the total number of variants. Specifically, I had question about the out_mode option.
below is a sample code of our UnifiedGenotyper,
java -Xmx8g -Djava.io.tmpdir=/tmp/evm-gatk/ \ -jar /medpop/mpg-psrl/Parabase/Tools/GenomeAnalysisTK-2.3-9-ge5ebf34/GenomeAnalysisTK.jar \ -T UnifiedGenotyper \ -R /medpop/mpg-psrl/Parabase/hg19/ucsc.hg19.fasta \ -I /medpop/mpg-psrl/Parabase/Projects/final/final.list \ -o /medpop/mpg-psrl/Parabase/Projects/final/S284.snp.small.vcf \ -stand_call_conf 50.0 \ -stand_emit_conf 10.0 \ -out_mode EMIT_VARIANTS_ONLY \ --dbsnp /medpop/mpg-psrl/Parabase/hg19/dbsnp_137.hg19.vcf \ -l INFO \ -A DepthOfCoverage \ -A HaplotypeScore \ -A InbreedingCoeff \ -A LowMQ \ -glm SNP \ -dcov 200 \ -nt 4 \ -nct 3 \ Thanks