Polymerase chain reaction (or PCR for short) is a technique to rapidly copy a small section of DNA into thousands to millions of copies. It can be used to enhance low count DNA samples; especially in-situ on a plate used for DNA testing. The problem is it can introduce errors in making the copy. And if the first copy has an introduced error, thousands more with that error will be introduced. A common error in PCR that can occur is known as stutter in CNV regions; where more or less repetitions are copied. PCR is heavily used in enrichment during WES sample preparation as well as for in-situ replication on a plate to increase the near volume of identical DNA strands (for increasing the "signal" from the photographic image of the plate).
The desire is to have PCR free sequencing. PCR duplicates can usually be detected in NGS by there existing a pile-up of the same read segments aligned to the same location and being identical in length and content. All but one of the "duplicates" are kept for analysis and VCF creation. The others are marked as invalid. Samples with duplicate rates of read segments over 5% (often due to PCR) are considered unreliable in clinical analysis.
The desire is to have PCR free sequencing. PCR duplicates can usually be detected in NGS by there existing a pile-up of the same read segments aligned to the same location and being identical in length and content. All but one of the "duplicates" are kept for analysis and VCF creation. The others are marked as invalid. Samples with duplicate rates of read segments over 5% (often due to PCR) are considered unreliable in clinical analysis.