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Old 07-10-2012, 02:11 AM   #1
bioinf newbie
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Default How to compute percentage of my genome covering human reference genome?

I have the alignment file for my genome (bam).
I want to find out % of genome that covered reference human genome with atleast 1 read, 2 reads, 3 reads, and 4 reads.
How do I go about it?
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Old 07-10-2012, 04:03 AM   #2
svl
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Maybe this can help you:
http://www.broadinstitute.org/gsa/wi..._Coverage_v3.0

Requires some work to get it working properly and also I think the documentation is not that clear about what it calculates precisely, but when using the option "-geneList" it outputs what you want (% covered by 1/2/3/50/100/etc)
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Old 07-10-2012, 04:16 AM   #3
colindaven
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Have a look at the samtools depth command too if you struggle with GATK.
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