I'm trying to eliminate inserts larger than 500 bp in a Bam file generated by Bowtie2 using the Filter BAM app in BAMTools (filter on insert size <=500). The largest read reported for the input Bam file is 81267 bp; hence, I want to delete all reads between 501 and 81267 bp. When I use the Picard tools to analyze insert sizes of the input and output files, the reported insert sizes are identical. I can't determine why Picard seems to see the large inserts, but BAM tools seems not to see them. Any help is appreciated.
More info via email: The data is ChIP-seq