May I ask for your suggestions to correct allele frequencies for SNVs from WGS samples. In more detail, tumors and matched normal data were aligned to hg38 with BWA mem, followed by variant calling with VarScan. SNVs were then filtered with the recommended fpfilter and required not to overlap with the latest 1KG variants. As pathology estimates for the tumor samples range between 50 and 70%, the obtained allele frequencies should be corrected for these impurities and copy number. I browsed through the posts out there on this topic and as always, 1 one question, many answers. Could you therefore give your opinions on which tool currently sets the standard for SNV classification?
Question: Correcting SNV allele frequency
16 months ago by
ATpoint ♦ 14k
ATpoint ♦ 14k wrote:
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