I generated BAM files using the STAR RNA-Seq aligner and the work stream described in GATK:
My R command with the error I am running into with these BAM files:
> heterozygotePositions <- scanForHeterozygotes(reads, maxReads=1e+07, verbose=T)
Investigating chromosome chr4
Investigating sample 1 out of 33
Error in new[start[i]:(start[i] + length(toKeep[[i]]) - 1), i] <- charList[[i]][toKeep[[i]]] :
number of items to replace is not a multiple of replacement length
I would appreciate some help with this error.