I have 6 datasets for 3 individuals (forward and reverse DNA seuqences) that I am trying to identify polymorphic sites in reference to the human genome. I have performed FastQC, Fastq Groomer, Map with Bowtie for Illumina, addorreplacereadgroups, mergeSAMfiles, and performed FreeBayes and performed VCFfilter for -f "QUAL > 40". I am not seeing any insertions or deletions when looking at the FreeBayes data or when filtering for insertions or deletions. Other filters seem to be working such as filtering for snps, mnps, complex, and such. Does anyone know why I cannot see any indels in my output? Thanks in advance!