Fig 1.
Visualization of the bit flag system.
If a variant pair could be phased, it is either labeled as cis or trans. Additionally, it can be labeled as innocuous. If a variant pair could not be phased, there was either too little evidence for calling cis or trans or one of both variant alleles could not be found in the mapped reads.
Table 1.
Benchmark results of SmartPhase and WhatsHap.
Fig 2.
Boxplots showing the distribution of relative amounts of pairs labeled as cis, trans, and innocuous (only for trio phasing) as well as the percentages of pairs that are cleared, confidently cleared after removing low quality phasing predictions, and pairs that can be excluded as being non-pathogenic.
The plots show results for SmartPhase using only read information for 800 singleton patients (a), using both trio and read phasing for 121 trio patients (b) and the results for the same individuals using physical phasing information provided by the HaplotypeCaller of GATK (c) & (d).
Fig 3.
Boxplots showing the percentage of cleared pairs for SmartPhase (SP) and WhatsHap (WH) in read only and in combined read & trio mode on the 21, 066 variant pairs identified in the 121 trio patients of the clinical WES data cohort.