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Old 09-28-2012, 05:36 AM   #3
Junior Member
Location: US

Join Date: Aug 2012
Posts: 3

Yes sorry I posted the wrong link. This what I have posted was my mpileup output.
Well sorry that I wasn't clear. I was just asking how I can set the minimum consensus quality. After the whole pipeline, there is a FQ listed in the info of the vcf file.

##INFO=<ID=FQ,Number=1,Type=Float,Description="Phred probability of all samples being the same">

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  bar
1     9778579   .       C       T       62      .       DP=17;VDB=0.0000;AF1=1;AC1=2;DP4=0,0,13,0;MQ=60;FQ=-66  GT:PL:GQ        1/1:95,39,0:75
1     9781412   .       C       G       214     .       DP=66;VDB=0.0768;AF1=1;AC1=2;DP4=0,0,37,15;MQ=55;FQ=-184        GT:PL:GQ        1/1:247,157,0:99
1     9782556   .       C       T       222     .       DP=368;VDB=0.0599;AF1=1;AC1=2;DP4=2,0,263,42;MQ=59;FQ=-282;PV4=1,0.27,0.36,1    GT:PL:GQ        1/1:255,255,0:99
I changed the script by now of the varFilter but I wanted to know if there is another way (w/o changing the script), because in the paper there was no changing at all and again: they used the same version of samtools, so I was just curious.
Thank you!

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