Fig. 3
From: Challenges in exome analysis by LifeScope and its alternative computational pipelines
Empirical cumulative distribution function (ECDF) of variant quality (QUAL) property assigned by GATK for variants identified in alignments produced by different mapping programs. To compute ECFD only variants that have been identified by all approaches together were used. ECDF’s of different alignments are color-coded: BFAST by blue line, LifeScope-GATK by black, MAQ by green and SHRiMP by red. Panels correspond to the family exomes. ECDF plots of QUAL per method in proband exome are on the top, the mother exome is in the middle and exome of the father is on the bottom. Median QUAL value of LifeScope-GATK consistently apears around 300 in all exomes. For BFAST-GATK it is around 200. Other approaches differ across the exomes