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Creating updated resources from gnomAD for somatic variant calling (Mutect2)
I want to call somatic variants in tumor-only mode with Mutect2. For the GRCh38 reference, in the GATK Resource Bundle I found the files
af-only-gnomad.hg38.vcf.gz (to remove germline muations) and
small_exac_common_3.hg38.vcf.gz (for the GetPileupSummaries and CalculateContamination commands for the filtering step).
I'd like to re-create these files using the last version of gnomAD files, both
gnomad.genomes.r2.1.1.sites.liftover_grch38.vcf.bgz, exploiting the command lines in your
I have two questions:
small_exac_common_3.hg38.vcf.gz have 227532 and 4749 variants with no PASS value in the FILTER column, respectively. Why are there in these two files the no-PASS variants? This let me think that I must not remove these variants.
2) The command
gatk SelectVariants -R reference.fa af-only-gnomeAD.vcf --select-type-to-include SNP -restrict-alleles-to BIALLELIC --selectExpressions "AF > 0.05" -O biallelic-gnomeAD.vcf.gz --lenient leads to a VCF file with AF values from 0.05 to 1. Why does the AF values range from 0.051 to 0.499 in the
Thank you for your hard work!