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
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