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low sensitivity in evaluation

mahyarheymahyarhey BostonMember

I used variant evaluation for getting some parameters such as concordance rate, sensitivity and specificity. In the following table it can be seen the rate of concordance & specificity is very good but the rate of "sensitivity" is very low. Is there any explanation or hint? I compared my VCF results of HaplotypeCaller with OMNI2.5 illumina bead chip.Thanks

Sample nEvalVariants nVariantsAtComp nConcordant concordantRate nVariantLoci nSNPs sensitivity specificity
sample0001_chr1 7249 6092 5971 98.01 7249 6761 0.73 99.99
sample0001_chr2 4669 4159 4107 98.75 4669 4343 0.46 100
sample0001_chr3 4789 4220 4154 98.44 4789 4481 0.55 100
sample0001_chr4 3139 2823 2787 98.72 3139 2914 0.36 100
sample0001_chr5 3670 3249 3199 98.46 3670 3397 0.47 100
sample0001_chr6 3969 3533 3376 95.56 3969 3675 0.49 99.99
sample0001_chr7 3879 3517 3449 98.07 3879 3645 0.56 100
sample0001_chr8 3336 3046 3009 98.79 3336 3145 0.50 100
sample0001_chr9 2820 2397 2348 97.96 2820 2621 0.50 100
sample0001_chr10 4011 3605 3561 98.78 4011 3721 0.66 100
sample0001_chr11 3111 2812 2767 98.40 3111 2877 0.52 100
sample0001_chr12 3276 2925 2881 98.50 3276 3026 0.57 100
sample0001_chr13 1733 1554 1535 98.78 1733 1608 0.39 100
sample0001_chr14 2005 1808 1781 98.51 2005 1849 0.52 100
sample0001_chr15 2364 2128 2102 98.78 2364 2211 0.68 100
sample0001_chr16 2997 2727 2676 98.13 2997 2828 0.84 99.99
sample0001_chr17 3308 2976 2914 97.92 3308 3098 1.07 99.99
sample0001_chr18 1341 1217 1202 98.77 1341 1245 0.40 100
sample0001_chr19 3740 3378 3304 97.81 3740 3489 1.44 99.99
sample0001_chr20 1763 1600 1582 98.88 1763 1652 0.67 100
sample0001_chr21 821 613 590 96.25 821 753 0.41 99.99
sample0001_chr22 2044 1816 1793 98.73 2044 1896 1.28 99.99
sample0001_chr23 674 582 567 97.42 674 604 0.17 100
Total 70708 62777 61655 98.2 70708 65839 4.47 100

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