Is there any way to get the coverage file from MuTect2? I am working on mutation rates, and I would really like to know how many sites for each tumor/normal pair are getting examined. Thanks!
Hi Justin (@justin_lack),
I believe you are asking for the intervals that the tool considers for graph assembly. Is this correct? If so, we call these regions ActiveRegions and have an optional --activeRegionOut or -ARO argument that will write out active and inactive regions to a file. The tool documentation provides more detail on the format of this file.
I hope this is helpful.
Yes, but more specifically, within these active regions, I want to know which positions are passing Mutect2 filters and are sufficiently covered to allow for comparison between the tumor and normal files. When I ran it with the --activeRegionOut flag, it appeared to just spit out the bed intervals I supplied with the -L option (these are the exome capture targets). So I am wondering if the --activeRegionOut flag is just telling me which sites are to be considered, or which sites are considered and ALSO are sufficiently covered for comparison between the two samples. Thanks!
If you're looking for something directly analogous to the WIGGLE file that was produced by the original MuTect, that is no longer available in MuTect2.
The ARO file specifies, within the targets that you provided, which regions were considered "active" (worth processing) and which were considered uninteresting (because all the reads were reference.
If you want to evaluate what regions were considered "callable" (ie had data that was good enough to use for calling) you could try running DiagnoseTargets.
Thanks for your help. Not sure if it's an option, but it would really be nice to have something analogous the WIGGLE file that the previous version produced. I would think that this would be of use to most MuTect2 users. Thanks again for your help!
for the downstream analysis with MutSig, it needs the wiggle file from mutect to process, is there a way to get around by using Mutect2 ?
Unfortunately, we cannot help you here. MuTect2 does not output an equivalent file to the Wiggle file from MuTect1.