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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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I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
Here are nine questions we think about, in roughly the order they matter, before...06-18-2026, 07:11 AM -
Data variability is still an issue in sequencing technologies despite the advances in reproducibility and accuracy of these platforms. But the problem does not originate in the sequencing itself, but in the previous steps, before the sample reaches the sequencer.
The first step is collection, followed by preservation and sample preparation for analysis. Most scientists overlook those steps, but not being careful might just be skewing the experiment’s results.
...06-02-2026, 10:05 AM
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