`To:
`Subject:
`Date:
`Attachments:
`
`John West
`Mark Pratt
`Comparing methods to determine SNP error rate
`Thursday, May 3, 2012 12:13:18 PM
`Methods to determine SNP error rate 3May2012 JW.pptx
`
`Hi Mark,
`
`I would like our accuracy development options to be prioritized by quantitation of errors by
`type & underlying mechanism. So far, I don't feel we have a handle on the SNP error rate, and
`the data we do have (Rick Dewey's MIE analysis from late 2010) seems to be very different
`from what Hugo et al found when comparing Illumina vs Complete Genomics. I took a few
`minutes and put together a slide with what seem to be some of the options to address this, and
`am attaching it here. Can we discuss this when you get a chance ?
`
`Thanks,
`
`John
`
`Personalis EX2037
`
`
`
`Determining SNP Error Rate
`
`Quartet data
`
`CEPH1463
`CGI data
`
`NA12878 SRA data
`
`MIE Analysis
`
`Link MIE rate to
`error rate & type
`
`Process with
`modern
`HugeSeq (done)
`
`VCF’s aligned
`across four
`family members,
`including non-
`calls, coverage,
`allele Q-scores
`
`MIE Analysis
`
`Link MIE rate to
`error rate, type,
`mechanism
`
`Comparisons
`Same library, two
`runs
`
`Same protocol,
`two libraries
`
`Broad HiSeq vs
`CGI (vs array ?)
`
`Max quality
`alignment by
`combining 10
`paired-end insert
`lengths & very
`high coverage;
`Then compare
`individual runs to
`this standard
`
`Single genome
`Where is
`coverage
`insufficient ?
`
`Where are
`allele Q-
`scores too
`low ?
`
`Tri-allelic /
`triple
`haplotype
`sites
`
`Allelic bias
`(requires
`very high
`coverage)
`
`CEPH1463
`family new
`data
`
`Comparison
`ILMN / CGI /
`Genotyping
`
`MIE path like
`quartet
`
`Personalis EX2037
`
`
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