I wanted to know if any of you has had any experience with software detecting very large inversion.
I have the .bam files from aligning illumina mate-pair on BWA-MEM, and I am looking for some analysis. Microarray was used to confirm four deletions 2 mbp - 8,mbp in size, and I wanted to see if there are any large inversions that result from the fragments in between the inversions.
Haven't had any luck with many of the structural detection software such as pindel, lumpy-sv, SV-Detect , and GASV, and delly. They have been able to detect around 70 - 100 bp inversions. Pindel has a maximum of 8 million bp and many detections.
Also wanted to ask if BWA-MEM or Bowtie mapping algorithms may have issues with mapping sequences with many large deletions (5 million base pairs) and possible inversions.
Thanks! *edited "insertion" when I meant to say inversion. Sorry for the confusion!