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Hello,
I can successfully load my VEP annotated VCF file using vcfToMAF function.

my_MAF <- vcfToMAF("vepAnnoted_Strelka.vcf", inputStrelka = 'SNV')

vepAnnoted_Strelka.vcf loaded successfully!
VCF to MAF conversion is in process...
VCF to MAF conversion has been done successfully!

Then, I am trying to run calTMB function on with OR without passing BED file.

TMB_value <- calTMB(my_MAF, bedFile = readBed("/Homo_sapiens.GRCh38.91.v2.bed"), assay = 'MSK-v1' )

But in both the case, I am getting the following error.

Error in str_replace_all(bedFile, "19", "38") :
object 'bedFile' not found
In addition: Warning message:
In readBedPanel(assay, genVer, maf) :
Bed files in CaMutQC are not accurate. The result serves only as a reference.

My file was mapped using GRCh38 genome and Strelka was used for variant calling.

Any help would be appreciated.

Thanks in advance.

Best,
Shawez