so basically I'm trying to replicate a pipeline to get metrics similar to Coverage Analysis Report plugin from Ion Torrent S5 and I think I'm missing something here because when I run this command

samtools view -F 0x40 -L target.bed final.bam | cut -f1 | sort | uniq | wc -l

I only get 2042179 reads

but when I go to the report than I get from the plugin I get this

the total assigned amplicon reads is what I'm trying to get.

basically I have a bed file with every amplicon but when I use it to get the reads from that target I get less reads than I should