Hi Friends,
We are using NGS data from TSACP illumina 48 gene amplicon panel for diagnostic purpose. The data analysis results into lot of variants lying in the "homopolymer and repeat regions" with very good number of supporting reads. The Base Quality, Mapping Quality, Strand Bias and other parameters are all behaving like normal variants. What is the confidence level for caling such variants a "Significant Variant". Some are also known SNPs in SNP database.
Any comments regarding this will be grateful.
Cheers Satish
We are using NGS data from TSACP illumina 48 gene amplicon panel for diagnostic purpose. The data analysis results into lot of variants lying in the "homopolymer and repeat regions" with very good number of supporting reads. The Base Quality, Mapping Quality, Strand Bias and other parameters are all behaving like normal variants. What is the confidence level for caling such variants a "Significant Variant". Some are also known SNPs in SNP database.
Any comments regarding this will be grateful.
Cheers Satish
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