I am using Pindel in the -i bam_config.txt mode, on an Illumina paired-end BAM file, then converting to VCF using pindel2vcf. My mean insert size is 108. I am only interested in looking at chr3:36422675-38128073. I have 2 questions:

(1) For this chromosomal range, I get 30 inversions. This seems like too many to be real. Is there any reason why I would get so many inversions?

(2) One of the inversions occurs in the exonic range for MLH1, which I am interested in. However, Pindel did not return any zygosity or read depth for this case (blank). What is the reason for this?

Thank you very much in advance.