Hi, I’m using bedtools to find regions of<20x coverage of target areas for a .BAM generated by IonTorrent server. The result obtained is different from the coverage track in IGV for a given .BAM – often a couple of reads more for a given position obtained by bedtools. Thus, my regions of <20x coverage are smaller than what I see in IGV. I’m assuming that coverage track in IGV doesn’t take into account filtered reads while bedtools does? Can I run bedtools only on filtered reads? How can I see all reads in IGV? thanks!
Question: Difference in BAM coverage between bedtools output and IGV coverage track
10 weeks ago by
myology • 0
myology • 0 wrote:
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