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Phasing for medical sequencing using rare variants and large haplotype reference panels.

Sharp K, Kretzschmar W, Delaneau O, Marchini J - Bioinformatics (2016)

Bottom Line: Compared to other approaches that do not explicitly use rare variants we obtain significant gains in phasing accuracy, less variation over phasing runs and improvements in speed.For example, using a reference panel of 7420 haplotypes from the UK10K project, we are able to reduce switch error rates by up to 50% when phasing samples sequenced at high-coverage.These results represent a proof of concept that rare variant sharing patterns can be utilized to phase large high-coverage sequencing studies such as the 100 000 Genomes Project dataset.

View Article: PubMed Central - PubMed

Affiliation: Department of Statistics, University of Oxford, Oxford, UK.

No MeSH data available.


Related in: MedlinePlus

Comparison of switch error rates for trio parents. The box-plot compares the empirical distribution of switch error rates achieved by different methods in 20 different phasing runs of chromosome 20 averaged over the two trio parents. Two different numbers of copying states were used:  for a single, fixed window size of 0.5 Mb. Methods compared are SHAPTEITR and SHAPTEIT2 with and without use of MCMC. We also applied SHAPEITR using the rephased UK10K panel. All methods were run with and without use of PIRs
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btw065-F2: Comparison of switch error rates for trio parents. The box-plot compares the empirical distribution of switch error rates achieved by different methods in 20 different phasing runs of chromosome 20 averaged over the two trio parents. Two different numbers of copying states were used: for a single, fixed window size of 0.5 Mb. Methods compared are SHAPTEITR and SHAPTEIT2 with and without use of MCMC. We also applied SHAPEITR using the rephased UK10K panel. All methods were run with and without use of PIRs

Mentions: Figure 2 compares the performance of SHAPEITR with that of SHAPEIT2. SHAPEIT2 was run both with and without the use of MCMC. In addition, we ran all three methods with and without the use of PIRs. We also ran SHAPEITR using the rephased UK10K panel. Switch error rates are averages across the two trio parents. We use box plots to indicate the variability across the 20 different runs.Fig. 2.


Phasing for medical sequencing using rare variants and large haplotype reference panels.

Sharp K, Kretzschmar W, Delaneau O, Marchini J - Bioinformatics (2016)

Comparison of switch error rates for trio parents. The box-plot compares the empirical distribution of switch error rates achieved by different methods in 20 different phasing runs of chromosome 20 averaged over the two trio parents. Two different numbers of copying states were used:  for a single, fixed window size of 0.5 Mb. Methods compared are SHAPTEITR and SHAPTEIT2 with and without use of MCMC. We also applied SHAPEITR using the rephased UK10K panel. All methods were run with and without use of PIRs
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4920110&req=5

btw065-F2: Comparison of switch error rates for trio parents. The box-plot compares the empirical distribution of switch error rates achieved by different methods in 20 different phasing runs of chromosome 20 averaged over the two trio parents. Two different numbers of copying states were used: for a single, fixed window size of 0.5 Mb. Methods compared are SHAPTEITR and SHAPTEIT2 with and without use of MCMC. We also applied SHAPEITR using the rephased UK10K panel. All methods were run with and without use of PIRs
Mentions: Figure 2 compares the performance of SHAPEITR with that of SHAPEIT2. SHAPEIT2 was run both with and without the use of MCMC. In addition, we ran all three methods with and without the use of PIRs. We also ran SHAPEITR using the rephased UK10K panel. Switch error rates are averages across the two trio parents. We use box plots to indicate the variability across the 20 different runs.Fig. 2.

Bottom Line: Compared to other approaches that do not explicitly use rare variants we obtain significant gains in phasing accuracy, less variation over phasing runs and improvements in speed.For example, using a reference panel of 7420 haplotypes from the UK10K project, we are able to reduce switch error rates by up to 50% when phasing samples sequenced at high-coverage.These results represent a proof of concept that rare variant sharing patterns can be utilized to phase large high-coverage sequencing studies such as the 100 000 Genomes Project dataset.

View Article: PubMed Central - PubMed

Affiliation: Department of Statistics, University of Oxford, Oxford, UK.

No MeSH data available.


Related in: MedlinePlus