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-   -   Low Coverage using target enrichment on Ion Torrent (http://seqanswers.com/forums/showthread.php?t=67851)

reggiardo.anselmo 04-25-2016 06:50 PM

Low Coverage using target enrichment on Ion Torrent
 
Hi everybody.
Hope you can help troubleshooting this issue.
I used to carry our BRCA1/BRCA2 target enrichment using Ampliseq paneles. However, Ive recently changed to GeneRead panels by QIAGEN with very similar results.
Ive carried out about 12 runs but the last three samples I've run when I analyzed them using the QIAGEN web portal turned out to have a low coverage (around 40X) and a lot of previously unreported variantes. In previous samples the coverage was higher than 500X and variants were almost always the same for both genes.
Do you have any suggestion of why the depth has decreased and how this is related to an increased number of variants?
Could it be due to a wrong dilution of original library prior to OT2?

thanks!


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