Hi
I have noticed that during the production of my reference.cnn (panel of normals), cnvkit is incorrectly allocating female status to the male samples (I have a approximately equal mix of male and female sample data). The message is:
sampeN chromosomal X/Y ploidy looks like male in targets but female in antitargets; preferring antitargets
I can get around this (for all but one male sample) by removing the antitarget regions for the Y chromosome entirely (for all steps and subsequent analyses; target Y region left in situ). As such, I assume this issue may be related to low coverage on the Y chromosome (we only target the SRY gene on this chromosome ). Is this a valid work around or can this be fixed or addressed in a better manner? Eg make a female and male reference set separately then somehow merge together.
Hi I have noticed that during the production of my reference.cnn (panel of normals), cnvkit is incorrectly allocating female status to the male samples (I have a approximately equal mix of male and female sample data). The message is:
sampeN chromosomal X/Y ploidy looks like male in targets but female in antitargets; preferring antitargetsI can get around this (for all but one male sample) by removing the antitarget regions for the Y chromosome entirely (for all steps and subsequent analyses; target Y region left in situ). As such, I assume this issue may be related to low coverage on the Y chromosome (we only target the SRY gene on this chromosome ). Is this a valid work around or can this be fixed or addressed in a better manner? Eg make a female and male reference set separately then somehow merge together.