Entering edit mode
9.6 years ago
Satish Gupta
▴
40
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 calling such variants a "Significant Variant". Some are also known SNPs in SNP database.
Any comments regarding this will be grateful.
Cheers
Satish :)
Well think about it this way, if you have an exactly repeating region and a read that could match both places exactly then you cannot possibly know where the read is coming from. Hence you could not establish from the alignment alone where the variant is located. You would need to use extra information to establish that.