I am currently working on estimating tumour mutational burden using the RNA-Mutect-WMN pipeline. The process requires an output from RNA-Mutect, which in turn needs the output of Mutect2.
I have proceeded with the following steps:
1.Acquired tumour RNA-seq fastq files.
2.Executed Mutect2 in tumour-only mode to generate a VCF file.
3.Performed filtering on the VCF and subsequently annotated it using Funcotator (a successor to Oncotator), resulting in MAF files
4.Used the aforementioned MAF file for RNA-Mutect
The initial steps with RNA-Mutect run smoothly, but I encounter issues during the filtering step where MATLAB files come into play. I receive errors related to mismatched column names, and the row numbers do not align as expected. I attempted using other annotators such as VEP and Annovar, but they do not yield the required columns for compatibility.
A specific challenge is the FilterRNAMutationsNoPoN binary executable; since the source script isn't available, troubleshooting is proving to be difficult.
Could anyone provide insights or suggestions on how to resolve these discrepancies and proceed with the workflow? I would greatly appreciate any guidance.
Thank you!
Following is the error I am encountering :
Error using intersect
Inputs A and B must be matrices with the same number of columns in the 'rows' case.
Hello ,
I am currently working on estimating tumour mutational burden using the RNA-Mutect-WMN pipeline. The process requires an output from RNA-Mutect, which in turn needs the output of Mutect2.
I have proceeded with the following steps:
1.Acquired tumour RNA-seq fastq files. 2.Executed Mutect2 in tumour-only mode to generate a VCF file. 3.Performed filtering on the VCF and subsequently annotated it using Funcotator (a successor to Oncotator), resulting in MAF files 4.Used the aforementioned MAF file for RNA-Mutect
The initial steps with RNA-Mutect run smoothly, but I encounter issues during the filtering step where MATLAB files come into play. I receive errors related to mismatched column names, and the row numbers do not align as expected. I attempted using other annotators such as VEP and Annovar, but they do not yield the required columns for compatibility.
A specific challenge is the FilterRNAMutationsNoPoN binary executable; since the source script isn't available, troubleshooting is proving to be difficult.
Could anyone provide insights or suggestions on how to resolve these discrepancies and proceed with the workflow? I would greatly appreciate any guidance.
Thank you!
Following is the error I am encountering :
Error using intersect Inputs A and B must be matrices with the same number of columns in the 'rows' case.
Error in intersect
Error in ExacPlusEditingFiltering (line 6)
Error in FilterRNAMutationsNoPoN (line 115)
MATLAB:INTERSECT:AandBColnumAgree