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Population frequency in MuTect2
I am running MuTect2 with GATK4 in tumor only mode but the SNPs in my vcfs are not labelled with their rs number or population frequency. Here is the command I am using.
gatk Mutect2 \ -L intervalfile.bed \ -R ucsc.hg19.fasta \ -I sample.bam \ -tumor sampleid \ --germline-resource dbsnp_138.hg19.vcf \ -ip 20 \ -O variants.vcf
CHROM REF ALT ID TLOD AC FILTER POS POP_AF chr4 A G . 3458.76 NA PASS 55946081 5.000e-08 chr4 A G . 2806.25 NA PASS 55948108 5.000e-08 chr4 A C . 1399.17 NA PASS 55968053 5.000e-08
If I use the GATK VariantAnnotator I am able to get rs number but the population frequency shows up as 5E-8 (even with --resource-allele-concordence set to true). Why is MuTect2 (and VariantAnnotator) not labelling rs number and pop frequency?
gatk VariantAnnotator \ -V variants.vcf\ -O annotatedVariants.vcf \ --dbsnp dbsnp_138.hg19.vcf \ --resourceMills_and_1000G_gold_standard.indels.hg19.sites.vcf \ --resource 1000G_phase1.snps.high_confidence.hg19.sites.vcf \ --resource-allele-concordance true
CHROM REF ALT ID TLOD AC FILTER POS POP_AF chr4 A G rs4421048 3458.76 NA PASS 55946081 5.000e-08 chr4 A G rs2412617 2806.25 NA PASS 55948108 5.000e-08 chr4 A C rs7655964 1399.17 NA PASS 55968053 5.000e-08