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Old 10-05-2012, 05:04 AM   #1
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Location: UK

Join Date: Feb 2011
Posts: 4
Default PCR-based target resequencing with Illumina

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.

ugm6hr is offline   Reply With Quote

fluidigm, gatk

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