Igv

[mmmm]

I am using IGV to view the mapped bam file to the reference- some genes have no coverage at all (no grey bars)- how could I know if these regions are absent from my genome (compared to the reference) or they were not sequenced at all?

[GenoMax]

You are not going to know for sure from data you have at hand. Here are a couple things to consider.

If you have good coverage on either side of the region you are not seeing then there is a chance that the region is absent in your genome (you will need to verify by additional experimentation).

If you do not have uniformly good depth of coverage across the genome then you would not know if a particular region was not sequenced. You would probably need to sequence deeper in that case.

[mmmm]

Igv

You are not going to know for sure from data you have at hand. Here are a couple things to consider.

If you have good coverage on either side of the region you are not seeing then there is a chance that the region is absent in your genome (you will need to verify by additional experimentation).

If you do not have uniformly good depth of coverage across the genome then you would not know if a particular region was not sequenced. You would probably need to sequence deeper in that case.

Yes- this makes sense
I was wondering why I can see in IGV white bars at certain regions (not grey bars)?

[dpryan]

Their MAPQ is 0 (otherwise, they're grey or another color).

[dpryan]

Also, have a read through the IGV documentation, it's pretty good in this regard.

[Bukowski]

Is this exome capture? If so I would check the regions are captured by the kit used in the first place. The bed files for the capture regions will be available from the manufacturer, and it may be that the regions might not be sequenced for this reason.