dpclust3p for INDELs

[tobyaicher]

Hi,

Is it possible to run DPclust3p on INDELs that are present in a VCF file (from mutect2 output)?

From looking through the code I think the issue is that the runGetDirichletProcessInfo function requires the count input to be in the format of A,T,C,G counts and not REF count vs. ALT counts. INDELs counts could fall in format of REF vs. ALT counts but can't be coerced into A,T,C,G counts.

I imagine the dumpcountsFromVCF function would have to be re-written to give REF vs. ALT count output format, and then runGetDirichletProcessInfo have to be re-coded to accept this input format.

Do you know of anyone who has done this? Do you have any suggestions for how to get DPclust3p information for INDELs? I don't need to actually run all of DPclust on the INDELs, just DPclust pre-proprocessing as I am just interested in site copy number and the multiplicity of the INDELs.

Thanks

[tobyaicher]

To follow-up: It looks like runGetDirichletProcessInfo immediately converts the Construct_Allelecounter format (A,T,C,G count format) into a WT vs. Mut count format (using the getWTandMutcount function). It seems like to call INDELs you could just modify the AllelCounts.mutect function and the getWTandMutcount function so that you don't need to go through intermediate of A,T,C,G counts and instead just get WT and Mut counts directly from the VCF, which would be compatible with INDELs.