Good day
I have run the XHMM pipeline in in order to ID CNV's from 9 sample exome sequences. Unfortunately the .vcf file was empty. I assume this may either mean that there are no CN variants within these samples or that something had occurred during the run which influenced my probability of success.
I therefore turn to you.
Is there anything that I could change in the params.txt document or other previous steps, that may improve my chances of success?? I unfortunately do not have have any reference to turn to that thoroughly explains the parameters in this txt file.
OR
is it a case of not having enough samples to significantly identify CN variants?