Hi, I used GATK germline variant calling pipeline to call short variants on paired end fastq files. After got the final analysis ready vcf, applied some extra filters, I inspected bam files in IGV for those variants of interest and found some strange things for one sample. Two variants of interest in this sample can only be found on inversion reads.
In this first graph, the alternative allele G can only be found in RR and LL reads (blue color) in IGV. 13 out of 15 inversion reads have this G allele.
In the second graph, similarly, the alternative allele T can only be found in inversion reads. All the inversion reads have this T allele.
Further, I realized that all the inversion reads have same size shown in figure 3.
I wonder if these inversions are true inversions or they are artifacts (given all the same size) thus the variants only found on these reads are also not real.