mapped reads on target from samtools and Ion Torrent

Question

[ntrjferreira]

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