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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