Varscan2 mutational calling analysis
Hello, I have basic question in varscan2 mutation calling. varscan2 divide total SNPs into germline, somatic, LOH and unknown based on allele frequency. My question is if all 3 genomes (i.e. hg19, blood and tumor) have different nucleotide (at same position), where do that SNP should be classify? For e.g. 10th position of Chromosome 1 have "A" in hg19, Blood sample have "G" and tumor have "T". Coverage is adequate in both blood and tumor sample. Where do I classify this type of mutation?
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nilesh.gardi2688 •
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I think there is a miss understood between SNP and SNV variant. But if i'm wrong about miss understood, SNPs is defined from population frequency. So to get this kind of information you need databases like dbSNP gnomAD ExAC etc
I would call that a somatic mutation because it differs from your germline.