Open bredelings opened 3 years ago
It does seem that I could just generate a --refcall=POSITIONAL
or --refcall=BLOCKED
VCF file in addition to the polyclone VCF file to get the relevant information.
It looks like the --refcall option has no effect with polyclone.
Right, the --refcall
functionality is currently only implemented in the individual
calling model, and even here I wouldn't claim that it's fully functional - there are some serious performance issues. I'm yet to settle on a model - it's a really difficult problem - hence why it hasn't been implemented in other calling models.
Thanks! That makes sense.
Describe the bug It looks like the
--refcall
option has no effect with polyclone.Am I missing something, or does refcall not work with polyclone?
If it is not there, is there a specific issue (e.g. finding haplotypes for non-variant positions) that is preventing this, or is the information all there and just not printed?
(The context is that I'd like to distinguish between non-variant sites where reads support the reference, and sites where there is no coverage. So, perhaps using the AD field or the DP field.)
Version
Command line to run octopus: