I was using TEQC to do quality control of my WES bam files aligned by bwa-mem.
My data are paired end, so a function reads2pairs
is called to make the paired-end reads to be a single fragment.
I then get this error:
> readpairs <- reads2pairs(reads)
Error in reads2pairs(reads) : read pair IDs do not seem to be unique
I asked in the bioconductor support site and went to the source code of that function.