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Samtools depth caps coverage values at around 8000.
I merged together a few bam-files to look at total coverage. I had a hard time understanding why all the different chromosomes had maximum coverage values of around 8000 (between 8015-8053 approximately).
When I googled for potential reasons why, I stumbled across this bug report: http://sourceforge.net/mailarchive/m...sg_id=28166483
and downloaded the patch attached. Now samtools depth works as it should.
A big heads up to everybody calculating coverage based on samtools! You may get wrong values! I can't help why wonder why the samtools developers haven't released a new samtools version with this bug fixed yet.
I merged together a few bam-files to look at total coverage. I had a hard time understanding why all the different chromosomes had maximum coverage values of around 8000 (between 8015-8053 approximately).
When I googled for potential reasons why, I stumbled across this bug report: http://sourceforge.net/mailarchive/m...sg_id=28166483
and downloaded the patch attached. Now samtools depth works as it should.
A big heads up to everybody calculating coverage based on samtools! You may get wrong values! I can't help why wonder why the samtools developers haven't released a new samtools version with this bug fixed yet.