Hello, I am new to using bioconductor and new to genetics in general- sorry if this is an obvious question. I am trying to get started using the SomaticSignatures package. I have several TCGA subjects with .vcf files, and each subject has a .bam sequence file. I understand I need to load both the sequence and the reference to calculate signatures.
First, I converted the .bam file to .fa, and generated an index, using samtools. Then, I loaded the data as follows:
fa_A <- FaFile("sub1.fa")
dat <- readVcfAsVRanges("sub1.vcf", fa_A)
vr_A = mutationContext(dat, fa_A)
The last line returns: Error in value[[3L]](cone) : record 1 (1:12837280-12837282) failed
as a starting point, can anyone tell me what this errors means?