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  • Illumina Truseq Exome 62Mb - variant metrics?

    Hey Everyone,

    I'm just curious what kind of variant metrics everyone obtains for the Truseq 62 Mb exome enrichment. I've only processed around 6 samples but there are ~40 K SNPs per sample and ~700 novel SNPs not in dbsnp135. Also, the ti/tv hovers around 2.5 - 2.6 and is even lower (2.3) for novel SNPs. Reading other forums, it seems like the TI / TVshould be around ~3? I'm thinking maybe this is because the TruSeq 62 Mb contains UTRs and splice sites which may be less conserved than just the exons?

    Any input would be appreciated!

    MC

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