Dear all,
we use the Broad best practice pipeline to call germline variants on Panel-seq data, i.e. our chip comprises the Omimom. Hence, it is not a small target set but significantly smaller than for instance common exome-seq.
The results are good so far, the mixture model plots look decent to me.
Here are my questions:
1. Is there any best practice for such panels?
2. I attached a file with the tranches plot for the SNPs, what do you think? Shall we increase the --ts_filter_level for SNPs to, say, 99.99 (it is now 99.9 as in the best practice for exome-seq)?
Thank you, Chris