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ensemble caller #14
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Arun; |
Thanks, I completely understand. A good start or so it seems Arun |
Arun; |
I agree. Will keep you posted on any updates. thanks |
sorry for closing and re-opening. Just realized there was another issue, which might not be relevant to the ensemble calling per se. Currently, I am using the ensemble caller for somatic calls based on mutect2, muse, vardict, strelka and caveman. I am asking the caller to report any calls in at least 2 variant callers. the issue I noticed is based on how each of the callers report the tumour and normal format fields. Here is the header field from each of these callers.
As you probably notice, mutect2 and muse report TUMOR as the last column whereas Caveman, Vardict and Strelka report Normal in the last column. ensemble caller also reports the TUMOR field in the last column, but maintains the order as present in the variant callers. Therefore when a variant is seen in, say caveman and vardict, the normal and tumour format fields get switched. I am not quite sure how to deal with this just yet. Seeing, if I can change the default occurrence of these TUMOUR and NORMAL in the variant callers. Thanks |
Arun; |
Hello Brad,
Yes, that's what I did. Modified the vcfs for sample ordering before
feeding into the bcbio ensemble calling.
Good to know it is automatically done with the pipeline!
thanks
Arun
…On Fri, Dec 16, 2016 at 6:06 AM, Brad Chapman ***@***.***> wrote:
Arun;
You will have to ensure samples have consistent sample ordering prior to
feeding into ensemble calling. Thank you for highlighting this requirement.
Somatic callers do have different behavior in terms of sample ordering and
naming, so this requires some work upstream to normalize. This is done
automatically in bcbio (https://github.com/chapmanb/bcbio-nextgen)
pipelines so is not a part of the more standalone ensemble calling here.
Hope this helps.
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Hello Brad,
I have a question/request about the output from running ensemble variant caller, specifially the format field. At the moment the ensemble vcf file reports the format field from the first file of 'n' where it appears. For example, if I input vcf files from mutect2, strelka, vardict, and muse as my input callers and the variant in question appears in mutect2 and strelka, the format field is reported from mutect2. So, there are cases where the format fields could appear from mutect2 or strelka or vardict (but not muse, if I require the variant to be in at least 2 callers). This implies that there is no uniformity in the format field anymore. Is there any way to fix this so that a specific set of format fields are reported irrespective of the input vcf files? This is probably not the easiest thing to do, but I thought I'd ask you anyway.
thanks
Arun
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