Hi Arumilli,
You have used the filter -q 30 and -Q 30 to filter bad reads. The DP is raw and
DP4 is filtered reads. Try removing these two filters to check whether DP and
DP4 is still different.
Best,
Xiaobin
On 09 Sep 2014, at 12:29, Arumilli, Meharji <[email protected]> wrote:
> Hi all,
>
> I have used mpileup and vcfutils to generate variants in my sample in the
> following way:
>
> samtools mpileup -ABugf ref.fa -q 30 -Q 30 -l target.bed -d 1000000 input.bam
> | bcftools view -bvcg - > sam.vcf
>
> bcftools view sam.vcf | vcfutils.pl varFilter -D 1000000 > samfilt.vcf
>
> The depth coulmns in the output more specifically, DP and DP4 differ greatly.
>
> chr8 16494616 . T C 21.10 PASS
> AC=1;AC1=1;AF=0.500;AF1=0.502;AN=2;DP=158;DP4=0,1,1,1;
> chr8 16553135 . T C 32.80 PASS
> AC=2;AC1=2;AF=1.00;AF1=1;AN=2;DP=67;DP4=0,0,1,1;
> chr8 16589121 . A C 59 PASS
> AC=2;AC1=2;AF=1.00;AF1=1;AN=2;DP=29;DP4=0,0,1,2;
> chr8 16606800 . A G 31.80 PASS
> AC=2;AC1=2;AF=1.00;AF1=1;AN=2;DP=45;DP4=0,0,1,1;
>
> For instance for the first variant, DP=158 and DP4=0,1,1,1. It was
> documented that DP is raw depth and DP4 is filtered depth but still it is a
> huge difference. Could someone comment on this huge discrepancy? On what
> basis the DP4 values are filtered?
>
> Any suggestion on optimum parameters to be used in the above commands are
> welcome!!
>
> Cheers
> Mehar
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