XHMM GATK exome sequencing deletions genome wide or selected genes ?

Question

[Floris Brenk]

Hi all,

To identify exonic deletions from exome sequencing data I want to use XHMM. However doing it genome wide will take long since I have over 400 samples. Is it also possible to do for a gene list were I only select the genes (and exons) that I want? Lets say about 90 genes? or do I get then biased results?

Thanks!

[Floris Brenk]

Yes, this is perfectly possible!

Just make sure to change the parameters file from:

1e-08   6       70      -3      1       0       1       3       1

to:

1e-3    2   70  -3  1   0   1   3   1