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Figure 4 | BMC Research Notes

Figure 4

From: Evaluation of SNP calling using single and multiple-sample calling algorithms by validation against array base genotyping and Mendelian inheritance

Figure 4

Individual genome comparison between GATK and CASAVA pipeline in 108 unrelated Qatari individuals. A, C, and E show comparison for unfiltered sets (CASAVA ALL, GATK ALL). B, D, and F show comparison for quality filtered sets (CASAVA PASS, GATK PASS). A and B show boxplots of 108 transition-transversion (TsTv) ratios for pipeline’s variants sets (CASAVA, GATK) along with pipeline specific (CASAVA ONLY, GATK ONLY). C and D show boxplots of 108 het-hom ratios for pipeline’s variants sets (CASAVA, GATK) along with pipeline specific (CASAVA ONLY, GATK ONLY). E and F show barplot of average variant counts for 108 individuals with error at the top of each bar.

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