Closed oliverartz closed 2 years ago
It seems like the deconvolution of the DBS78 causes the issue. I reckon there are not enough DINUCs in the VCF, so the entire algorithm stops before getting to the IND step? If I try to manually skip the DINUC step by setting context_type="96,ID"
, I get the following error: Error in py_call_impl(callable, dots$args, dots$keywords) : KeyError: '96A'
. I am not quite sure how to tackle this issue. Has anyone reported this problem before and is there a known fix?
Hi @oliverartz,
It looks like there may have been some issues with generating your matrices. Did you install the mm10 reference genome? If you did and are still experiencing the issue could you please e-mail me some VCF files that can reproduce this?
Thanks!
Thanks for the help! I double-checked the mm10 reference genome and it is installed. It is interesting that I only get this problem with certain VCFs. Your response prompted me to generate the matrices first using SigProfilerMatrixGenerator and use those as input for SigProfilerExtractor, which worked great for SBS96, DBS78, and ID83. Using SigProfilerExtractor on the VCF does not work though. I have tried using the R wrapper first and then the Python version. I am sending you the VCF via email.
Thanks again 👍
Dear developers,
I have been using SigProfilerExtractor to extract mutational signatures for a number of VCF files. For two of those files, no ID signatures were produced and the script exited with an error:
ValueError: operands could not be broadcast together with shapes (78,0) (0,0)
I do, however, get the deconvolution for SBS and DBS for those samples.
The VCF files contain INDELs as the first lines of the output indicate
Starting matrix generation for SNVs and DINUCs...Completed! Elapsed time: 2.3 seconds. Starting matrix generation for INDELs...Completed! Elapsed time: 1.8 seconds. Matrices generated for 1 samples with 0 errors. Total of 395 SNVs, 4 DINUCs, and 109 INDELs were successfully analyzed.
This is the content of the
JOB_METADATA.txt
Thanks for your help!