Fig 1.
INDEL calling workflow in WES.
INDELs were called using four algorithms: GATK, SAMtools, Dindel, and Freebayes. Analysis pipelines and workflow systems are shown.
Table 1.
INDELs called and validation in four algorithms.
Fig 2.
Number of INDELs called by the four algorithms.
(A) INDELs were called using four algorithms: GATK, SAMtools, Dindel, and Freebayes. (B) Histograms of insertion (right) and deletion (left) counts by INDEL size. Counts were adjusted within each algorithm to account for the fraction of polarizable calls. (C) Accuracy of detection of INDELs in the four algorithms.
Table 2.
Validation of the four algorithms used for INDEL calling with WES and Sanger sequencing.
Table 3.
Comparison of INDEL-calling algorithms.
Fig 3.
Performance versus detected INDELs and PPVs.
(A) Concordance of INDEL detection between the four algorithms: GATK, SAMtools, Dindel, and Freebayes. Venn diagram showing the numbers and percentages of shared INDELs from the four algorithms: 4 algorithm intersection INDELs, 3 algorithm intersection INDELs, 2 algorithm intersection INDELs, and algorithm-specific INDELs. (B) Validation rates and PPVs of the intersecting INDELs between algorithms. The sensitivity increases at higher intersecting algorithms.
Fig 4.
Sources of INDEL detection error from WES.
(A) Number of validated INDELs in the following INDEL size. (B) Percentages of homozygous, heterozygous, repeat, and non-repeat in the validated and not validated set. (C) PPVs of error sources, 1) heterozygous, 2) repeat INDELs in all and GATK & SAMtools intersecting call set.