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Old 04-16-2012, 06:22 AM   #1
Marie_Noir
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Location: Berlin

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Default Read Depth in vcf (samtools / bcftools)

I generated one vcf file from 4 different bam-files (4 samples) and had a look at some variants in the vcf and in the IGViewer (IGV).

I don't understand why the value for DP in the formatstring (i.e. for one sample) often differs (is less) from what I can see in the IGV. Meaning, vcf tells me a certain variant in a certain sample has read depth (DP) of 3 but I see more reads covering that position in the IGV. I thought that maybe bases of bad quality where left out, but reads and base qualities are good. Is there any other measure that I don't know yet which filters out certain reads / bases from being reported in the DP field in the format string (and consequently is not used for genotype assignment)?

Any hint is appreciated.
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Old 04-17-2012, 07:48 AM   #2
baika
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Default

I also had same question when I started my analysis. Then I figured out that DP (Depth of coverage) is not exactly the "counts of reads" at that position. Please see following links and I am sure you will get the answer:
http://www.illumina.com/Documents/pr...alculation.pdf
http://www.illumina.com/truseq/quali...tribution.ilmn

Hope it helps
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