PCR-based target resequencing with Illumina

[ugm6hr]

I have enriched exonic regions of candidate genes with Fluidigm Access Array (microfluidic PCR-based) to create libraries from human DNA. The resequencing is on Illumina HiSeq.

Does anyone have experience of variant calling issues with PCR-based enrichment on Illumina sequencing data? We cannot remove / mark duplicates as we would normally with GATK, due to the target enrichment process. I'm unclear what effect this has on variant call quality metrics.

Thanks.