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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
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

Best Answer


  • Thank you! I see it now. As a side note, I had initially tried using the af-only-gnomad files from the bundle, but I am using hg19 for the bulk of my analysis and using the b37 files gave an error. I saw some mention of a liftover for converting the b37 vcf for use on the hg19 assembly but I can't find a link. Do you know how I could do this?

  • shleeshlee CambridgeMember, Broadie ✭✭✭✭✭

    You're welcome @dasnellings. For hg19 <--> b37 conversion, you can use LiftoverVcf. You will have to obtain a chain file. Alternatively, there are some threads on the forum discussing how to use sed to inline +/-chr. You'll have to search to find these.

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