mapped reads on target from samtools and Ion Torrent
Entering edit mode
9 weeks ago

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

enter image description here

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

samtools reads • 179 views

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