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Computational method to estimate the PCR duplication rate in high-throughput DNA sequencing experiments

PCR amplification is an important step in the preparation of DNA sequencing libraries prior to high-throughput sequencing. Existing computational methods for analysis of read duplicates assume that all read duplicates arise due to PCR amplification. However, a high rate of read duplicates is observed in deep sequencing experiments or experiments such as RNA-seq. We present a computational method that exploits the heterozygosity in diploid genomes to estimate the PCR duplication rate accounting for read duplicates that are not due to PCR amplification.

A paper describing this method has been published in BMC Bioinformatics, March 2017:

INPUT files for running program

  1. coordinate sorted BAM file with aligned reads
  2. VCF file with heterozygous variants called from BAM file using a variant calling tool such as GATK UnifiedGenotyper or samtools

compile the CODE

run 'make all'

Two step process to extract reads overlapping variant sites and then analyze read clusters to estimate PCR duplication rate

  1. ./extract_duplicates --bam sample.bam --VCF variants.VCF > sample.hetreads
  2. python -i sample.hetreads -f exome > sample.PCRdups

obtain FINAL estimate of the PCR duplication rate

grep FINAL_PCR_RATE sample.PCRdups > sample.PCRduprate.estimate

Sample Data

see DATA folder


  1. The program uses samtools (v 0.1.18) to parse BAM files. The source code for samtools is included in the github repository (directory parsebam/samtools-0.1.18).
  2. The program has been tested on exome-seq, targeted DNA seq and RNA-seq datasets. For RNA-seq, an independent set of heterozygous variants is needed.


method to estimate PCR duplication rate from high-throughput sequencing data



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