Question: Samtools Vcf Format Depth Discrepancy?
1
gravatar for Zev.Kronenberg
7.9 years ago by
United States
Zev.Kronenberg11k wrote:

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 • 3.6k views
ADD COMMENTlink modified 7.9 years ago by Deniz0 • written 7.9 years ago by Zev.Kronenberg11k
6
gravatar for Jeremy Leipzig
7.9 years ago by
Philadelphia, PA
Jeremy Leipzig18k wrote:

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

GT:1/1
PL:93,12,0
DP:4
SP:0
GQ:21
ADD COMMENTlink modified 7.9 years ago • written 7.9 years ago by Jeremy Leipzig18k

Sorry, I accidentally highlighted the wrong field. How are high quality reads defined? Seems odd not to count the total reads per individual...

Thanks

ADD REPLYlink written 7.9 years ago by Zev.Kronenberg11k

I think phred >=20

ADD REPLYlink written 7.9 years ago by Jeremy Leipzig18k
0
gravatar for Damian Kao
7.9 years ago by
Damian Kao15k
USA
Damian Kao15k wrote:

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.

ADD COMMENTlink written 7.9 years ago by Damian Kao15k
0
gravatar for Deniz
7.8 years ago by
Deniz0
Deniz0 wrote:

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

Thanks

ADD COMMENTlink written 7.8 years ago by Deniz0

Pretty much used the defaults from SAMtools why?

ADD REPLYlink written 7.8 years ago by Zev.Kronenberg11k

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

ADD REPLYlink written 7.8 years ago by Deniz0
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