xAtlas calibration #138
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xAtlas calibration #138
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Contributor
mlin
commented
Aug 22, 2018
mlin
commented
- include P output field
- derive AQ from P instead of genotype likelihoods
- set min_AQ thresholds and turn on genotype revision
- set drop_filtered=false and improve FT/FILTER liftover fidelity
- set required_dp=1 (needed customized AlleleDepthHelper)
Prevent CLI from choking on >3-column BED files
…nstead of genotype likelihoods
The thread and memory budgets were not taking the desired default values when the user did not specify them on the command-line.
Entails a special version of AlleleDepthHelper to understand the xAtlas equivalent of AD
…exus into mlin-xAtlas-calibration
mlin
added a commit
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Aug 24, 2018
- include P output field - derive AQ from P instead of genotype likelihoods - set min_AQ thresholds and turn on genotype revision - set drop_filtered=false and improve FT/FILTER liftover fidelity - set required_dp=1 (needed customized AlleleDepthHelper) - VR combi_method=max
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