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Fig. 3 | BMC Bioinformatics

Fig. 3

From: Evaluation of variant detection software for pooled next-generation sequence data

Fig. 3

ROC Analysis on VCFs generated from ClinSeq eight sample, 50 % coverage pools with a total of 35.1x depth of coverage, on average, with eight pools per program run. For CRISP and GATK, quality score filtering was gradually increased on a logarithmic scale (0–100,100-1000,1000-10,000, etc.) to obtain a full range of sensitivity and false positive scores. LoFreq’s filtering was incremented logarithmically up to 1000, then by 100 s since its quality score range was smaller than those of the other programs. Many of SNVer’s P-values were extremely small (with reported p-values as low as 0), so maximum p-value filtering was set at values from 10−10 down to 10−300. Full details of score thresholds used are contained in the worksheet titled “Supp Table S2 Main Paper Figure S3” in the Additional file 1: Figure S3

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