Samtools Vcf Format Depth Discrepancy?
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13.1 years ago

Here is a VCF line directly from the Samtools variant calling pipeline (no varfilter.pl) for one exome:

chr1    156713512       .       C       T       60.5    .       **DP=6**;AF1=1;AC1=2;DP4=0,0,4,0;MQ=34;FQ=-39       GT:PL:**DP**:SP:GQ  1/1:93,12,0:**4**:0:21

I noticed that the genotype column has a depth of 12 listed (highlighted: **). How can this be if DP=6? What am I missing?

vcf read samtools • 5.2k views
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6
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13.1 years ago

That 12 is not DP, DP is 4 (high quality bases)

GT:1/1
PL:93,12,0
DP:4
SP:0
GQ:21
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0
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Sorry, I accidentally highlighted the wrong field. How are high quality reads defined? Seems odd not to count the total reads per individual...

Thanks

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I think phred >=20

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13.1 years ago

In the [?]VCF specs[?]:

DP in info column (8th):

DP - combined depth across samples, e.g. DP=154

DP in genotype column (9th):

DP - read depth at this position for this sample (Integer)

One is for across samples and other is for this sample only.

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13.0 years ago
Deniz • 0

How did you get this vcf output? dafault setting gives GT:PL:GQ format. Could you write your command?

Thanks

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Pretty much used the defaults from SAMtools why?

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Your format is different. That's why I wondered. Are you happy with results and format?

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