SmartPhase: Accurate and fast phasing of heterozygous variant pairs for genetic diagnosis of rare diseases
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.