reference genome

[HengqiLiu]

Hi getzlab team：

What should I do to get mutsig2CV to run if the reference genome for my maf file alignment is hg38

Thank you！
Hengqi Liu

[julianhess]

Hi Hengqi,

Are you working with whole exomes or whole genomes? This will determine the reference files that you'll use.

—Julian

[HengqiLiu]

Hi Julian,

I am working with whole exome data from next generation sequencing.

—Hengqi

[julianhess]

In that case, please download the following reference files from Google Cloud using gsutil:

gs://getzlab-workflows-reference_files-oa/MutSig2CV/hg38/coverage_models.agilent.mat
gs://getzlab-workflows-reference_files-oa/MutSig2CV/hg38/target_list.gencode25.txt
gs://getzlab-workflows-reference_files-oa/MutSig2CV/hg38/context_and_effect_track.fwb
gs://getzlab-workflows-reference_files-oa/MutSig2CV/hg38/context_and_effect_track.fwi
gs://getzlab-workflows-reference_files-oa/MutSig2CV/hg38/covariates.agilent.txt

and populate a tab-delimited files called params.txt with the following:

skip_permutations       True
coverage_models_mat_file        coverage_models.agilent.mat
target_list_file        target_list.gencode25.txt
context_and_effect_fwb_file     context_and_effect_track.fwb
context_and_effect_fwi_file      context_and_effect_track.fwi
covariates_file        covariates.agilent.txt

Note that you need to either copy the reference files into the directory you're running MutSig from, or specify the full path to each reference file.

Then run MutSig by passing the path to the params.txt file as a third argument, as detailed here.

[HengqiLiu]

Thank you very much for your prompt help !!!

Best Wishes,
Hengqi Liu

[emucaki]

I apologize for re-opening this ticket, but is there credentials that I require to download the files listed above from the Google Cloud? I'm not experienced with 'gsutil', and all my attempts to download these files (with "gsutil cp" command) end in a "do not have storage.objects.get access to the Google Cloud Storage object" error. I'm not sure if its a problem with my setup or the files themselves.

Thank you.

[cbravo93]

I am having the same issue:

AccessDeniedException: 403 XXX@gmail.com does not have storage.objects.list access to the Google Cloud Storage bucket. Permission 'storage.objects.list' denied on resource (or it may not exist).
Any solution?

Carmen

[lh12565]

Hi, @julianhess Does the skip_permutations parameter have to be true for hg38 or optional? Thanks!