NextSeq indel Concordance with Plat genome or NIST
Hi,
I was wondering if anyone has had experience doing concordance with samples sequenced on nextseq machine. I'm finding the False Negative rate with indels to be high (15-19%), higher than for the hiseq.
I was using GATK GenotypeConcordance with both Platinum genomes and Nist truth sets. We sequenced the NA samples I forget the full name of it. Looks like out pipeline has a harder time with indels for nextseq vs. hiseq. thanks - Robert
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