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Greetings. I have found that in my particular data set that the most sensitive factor for true variants versus false positives is actually the DP4 (the total number) rather than the QUAL score or depth (DP). Is there a program or little script to filter by the total DP4? Thanks!
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filtering a VCF with javascript
I wrote a tool named vcffilterjs to filter a VCF using a javascript expression: See: https://github.com/lindenb/jvarkit#-...ascript-rhino-
Example:
wth
Code:function accept() { var DP4=variant.getAttribute("DP4"); if(DP4==null || DP4.size()!=4) return false; return DP4.get(0)+DP4.get(1)+DP4.get(2)+DP4.get(3)<10; } accept();Code:$ curl "https://raw.github.com/CBMi-BiG/snpEff/master/tests/vcf_homo.vcf" | \ java -jar dist/vcffilterjs.jar SCRIPT_FILE=filter.js 2> /dev/null
Code:(...) #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT s_1_ACAGTGA_sort.bam Y 3720217 . A G 8.65 . AC=2;AF1=1;AN=2;CI95=0.5,1;DP=2;DP4=0,0,0,1;FQ=-30;G3=4.415e-15,5.291e-06,1;MQ=38;SF=5 GT:GQ:PL 0/0:61:60,6,0 Y 3721230 . C G 21.80 . AC=2;AF1=1;AN=2;CI95=0.5,1;DP=2;DP4=0,0,0,2;FQ=-33;G3=1.456e-17,8.564e-07,1;MQ=29;SF=3 GT:GQ:PL 1/1:61:60,6,0 Y 3744605 . C A 3.98 . AC=2;AF1=1;AN=2;CI95=0.5,1;DP=2;DP4=0,0,0,2;FQ=-33;G3=1.468e-15,8.599e-07,1;MQ=19;SF=2 GT:GQ:PL 0/0:61:60,6,0 Y 9945223 . ATTT ATTTT 19.80 . AC=4;AF1=1;AN=4;CI95=0.5,1;DP=2;DP4=0,0,0,2;FQ=-40.5;G3=2.906e-18,8.564e-07,1;INDEL;MQ=45;SF=0,2 GT:GQ:PL 1/1:61:60,6,0
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@lindenb looks like just what I need, I'll let you know how it goes!Comment
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