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Distinct allele frequency patters by HaplotypeCaller and Mutect2 for the same sampleAnswered
I have analyzed a whole genome sequence of my sample (coverage = approx. x30) by HaplotypeCaller (a single sample) then Mutect2 (no matched control). The number of mutations (SNVs and INDELs) detec...
Why doesn't haplotypecaller use PON?
I am new to GATK and have just run HaplotypeCaller several times according to the best practice. I am now planning to try Mutect2 to compare my normal and tumor samples, but am rather confused by t...