Re: [Samtools-help] Why does varFilter filter this out?

[Barris, W. <Wes...@co...>]

Heng Li wrote on 2011-06-27:

> Strand bias

Thanks Heng.  I now see why the following variation was filtered out based on
strand bias:

chr10   1001844 .       C       T       134     .       DP=95;AF1=1;CI95=1,1;
DP4=12,0,28,49;MQ=20;FQ=-117;PV4=2.4e-05,1,1,1     GT:PL:GQ        1/1:167,90,0:99

I'm guessing it is mainly the difference in ref-forward versus ref-reverse reads.
However, the following variation is not filtered out by the same command.  There
is no PV4 field but the DP4 values appear worse.

chr10   452839  .       C       T       55      .       DP=11;AF1=1;CI95=1,1;
DP4=0,0,0,10;MQ=20;FQ=-57  GT:PL:GQ        1/1:88,30,0:57

Is the variation at 452839 really more likely a SNP than the one at 1001844?


> Heng
> 
> On Jun 27, 2011, at 5:34 PM, Barris, Wes wrote:
> 
>> I have a vcf file (attached) containing two variances.  Can anyone tell
>> me why the one at position 1001844 is filtered out by this command?
>> 
>> cat junk.vcf | vcfutils.pl varFilter
>> 
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>> Wes Barris
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