Tagged with #sensitivity
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Created 2015-07-30 15:44:28 | Updated | Tags: sensitivity variantevaluation
Comments (3)

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


Created 2015-07-16 18:45:45 | Updated | Tags: varianteval sensitivity specificity combiegvcfs
Comments (1)

I have 33 samples (VCF files) resulted from HaplotypeCaller and like to evaluate them using dbSNP as a comp to get concordance_rate, sensitivity, and specificity. One way is to evaluate each sample separately. Another approach is to combine all 33 files using "CombineGVCFs" and then evaluate one VCF file. Which of these 2 methods do you think is feasible and acceptable for variant evaluation? why? Thanks


Created 2015-05-15 15:20:56 | Updated | Tags: sensitivity variant-evaluation
Comments (13)

After I run --evaluationvariant, I got some values more than 1 for sensitivity. (e.g. 1.02, 1.59, 1.76, 1.42, etc.) My expectation for the sensitivity range is (0-to-1). How to interpret values of sensitivity greater than 1? Is that make sense?


Created 2013-11-30 15:32:34 | Updated | Tags: unifiedgenotyper haplotypecaller sensitivity
Comments (19)

Hi there,

I compared HaplotypeCaller and UnifiedGenotype of the latest version of GATK (2.7-4) on the same NA12878 trio. It seems HC missed some true variants (specifically, 7 out of the 49 experimentally validated de novo SNVs are missed). I guess this might be partly due to HCMappingQualityFilter, because the log says ~9% of the total reads have been filtered by this filter, and it looks there is not such a filter in UnifiedGenotyper. I wonder is there a safe way to relax HCMappingQualityFilter (default 20) to achieve a better sensitivity for HC?

Thanks in advance!

Aaron


Created 2013-02-02 15:23:08 | Updated 2013-02-02 22:49:30 | Tags: unifiedgenotyper vqsr haplotypecaller validation statistics sensitivity specificity
Comments (1)

Hi all, I've somewhere in this site that before VQSR the FP rate is expected to be around 10% (I guess for UnifiedGenotyper). Are there some updated statistics for VQRS? For HaplotypeCaller? For Exome/WG data? Another thing: we apply VQRS on all our analysis, we are trying to collect some validation statistics. We suspect that most of the FP have some particular "culprits" in VQRS (especially QD and MQ). Do you have some data about this? Best

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