Hello,
We are sequencing whole exomes (human) using an Illumina HiSeq2000. We previously did sample prep and exome enrichment using the Agilent SureSelect Human All Exon Kit. Recently we switched to the Illumina sample prep and exome enrichment kits, however we observed a dramatic increase in false positive SNP calls (the analysis pipeline is the same).
Has anybody else compared Agilent and Illumina exome enrichments and observed similar problems?
Thanks for any comments.
markusl
We are sequencing whole exomes (human) using an Illumina HiSeq2000. We previously did sample prep and exome enrichment using the Agilent SureSelect Human All Exon Kit. Recently we switched to the Illumina sample prep and exome enrichment kits, however we observed a dramatic increase in false positive SNP calls (the analysis pipeline is the same).
Has anybody else compared Agilent and Illumina exome enrichments and observed similar problems?
Thanks for any comments.
markusl
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