I generated BAM files using the STAR RNA-Seq aligner and the work stream described in GATK:

https://www.broadinstitute.org/gatk/guide/article?id=3891

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.

Thank you,

Joe

Hello,

Sorry to be late with my reply!

This error was solved some months ago, see https://github.com/pappewaio/AllelicImbalance/issues/3

Jesper