we are trying to call variants from a tumor sample using mutect2 (please find command used below)
In a tumor sample (that we are analyzing), we expect to see an amino acid missense variant at a position with multiple alternate alleles at low frequency. We found this when we investigated tumor bam file and it's not present in the corresponding normal. we are confident that mutation exists for a biological reason. Are there any specific filters within mutect2 that we can modify to see the expected variant?
Any help would be greatly appreciated!! Please let me know, if you need any further details.
Note: Mapping and base qualities of reads are very high for the samples we analyzed.
Thanks for your help!!
a) GATK version used : 22.214.171.124
b) Exact GATK commands used
/Software/GATK-126.96.36.199/gatk-188.8.131.52/gatk --java-options "-Xmx19g" Mutect2 --input normal.final.bam --input tumor.final.bam --normal-sample N_0196204 --tumor-sample T_0204565 --reference hg19_chr.fasta --output 0204565.mutect2.vcf --intervals FGFR_assay_high_plus_low_risk.sorted.merged.bed
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