XHMM GATK exome sequencing deletions genome wide or selected genes ? · Biostar

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XHMM GATK exome sequencing deletions genome wide or selected genes ?

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!

xhmm gatk genelist

• 2,389 views • link

updated 7.9 years ago by Ram

• written 10.5 years ago by 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

• 0 views • link

updated 7.9 years ago by Ram

• written 10.4 years ago by Floris Brenk

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