I first identified some somatic mutants with NGS. Then I validated them with Sanger sequencing. With NGS I also looked for loss of heterozygosity (LOH) in my tumor samples using a copy number analysis (CNV) approach (read count based). Some of the variants show LOH with the CNV analysis but not on the corresponding Sanger chromatogram.
From a quantitative point of view, which method (CNV or Sanger) would be the most accurate to detect LOH? Are the peaks on a Sanger chromatogram precise enough to asses the proportion of ref. vs alt. allele?