Closed ajitjohnson closed 4 years ago
Hello Ajit @ajitjohnson!
It is possible to set min VAF in
- algorithm:
min_allele_fraction: 1
https://bcbio-nextgen.readthedocs.io/en/latest/contents/configuration.html#somatic-variant-calling It is a post-calling filter: https://github.com/bcbio/bcbio-nextgen/blob/master/bcbio/variation/mutect2.py#L189
It was decided to have a common VAF limiting parameter for different callers: https://github.com/bcbio/bcbio-nextgen/issues/314
And, you may set individual parameters in the resource section of the yaml:
resources:
mutect2_filter:
- --minimum-allele-fraction
- 0.01
it will go into FilterMutectCalls
, a separate mutect2 step
https://github.com/bcbio/bcbio-nextgen/blob/a65f4b102ea42c83aa6cc7e2771285bc2fc73339/bcbio/variation/mutect2.py#L173
Are you sure --normal-lod
is this there?
https://gatk.broadinstitute.org/hc/en-us/articles/360035531132--How-to-Call-somatic-mutations-using-GATK4-Mutect2
https://gatk.broadinstitute.org/hc/en-us/articles/360036822431-FilterMutectCalls#--min-allele-fraction
The focus in bcbio was on supporting multiple callers (vardict, mutect2) in the somatic use case rather than exactly following GATK best practices, but given the extensive feedback from users I think it is optimised well.
You may see how exactly we call mutect2 here:
https://gatk.broadinstitute.org/hc/en-us/articles/360036822431-FilterMutectCalls#--min-allele-fraction
or from
cat bcbio-nextge-commands.log | grep mutect
in the end of your run.
We plan to outline this workflow step-by-step in the ongoing documentation improving effort here: https://bcbio-nextgen.readthedocs.io/en/latest/contents/internals.html#somatic-tumor-only-variant-calling-pipeline-with-umis-step-by-step
If you have any feedback on how to use mutect2 in bcbio better, let us know.
Sergey
Feel free to re-open if there are still issues.
Dear Team,
Is it possible to pass custom parameter values for the mutect2 variant caller? I would like to pass custom values for the following parameters.
--normal-lod and --minimum-allele-fraction
Also if I use mutect2, does it follow the other best practices that GATK recommends? If you have any documentation in that aspect, can you please point me towards that? Thank you very much.