Read coverage shows a difference in IGV
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23 months ago
jkim ▴ 170

Hello,

This is my bam file in IGV. There are way more reads mapped to the region 2 in the panel displaying reads. On the other hand, the coverage panel shows the opposite - there are more reads mapped to the region 1.

I also ran samtools depth and it said there are more reads mapped to the region 1. I am confused by this. Did IGV not show me all the reads mapped to the region 1 for some reason? I didn't change any setting for IGV.

bam

coverage BAM • 1.8k views
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may be the IGV algorithm collapsing reads generates a visual bias.

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I see. I will post this on the IGV help forum.

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perhaps it has something to do with the mapping quality? Image is a bit small but it seems there are much more gaps/indels/mismatches in region2 in stead of 1 ...

perhaps samtools only counts the well mapped reads or such?

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Well, I filtered reads out in my bam by mapping quality. Yeah, I will look into samtools depth more.

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I think I found why. If I unclick Downsampling option in alignment in preferences, it looks like IGV shows every read...

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23 months ago
GenoMax 144k

Check IGV preference settings for downsampling reads. Also if these are duplicate marked then check the setting for "do not show duplicates".

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Yeah, that is why. Thanks!

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