4168aaf280
Use case: The default AF priors used (infinite sites model, neutral variation) is appropriate in the case where the reference allele is ancestral, and the called allele is a derived allele. Most of the times this is true but in several population studies and in ancient DNA analyses this might introduce reference biases, and in some other cases it's hard to ascertain what the ancestral allele is (normally requiring to look up homologous chimp sequence). Specifying no prior is one solution, but this may introduce a lot of artifactual het calls in shallower coverage regions. With this option, users can specify what the prior for each AC should be according to their needs, subject to the restrictions documented in the code and in GATK docs. -- Updated ancient DNA single sample calling script with filtering options and other cleanups. -- Added integration test. Removed old -noPrior syntax. |
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| .. | ||
| annotator | ||
| beagle | ||
| bqsr | ||
| compression/reducereads | ||
| diagnostics | ||
| diffengine | ||
| fasta | ||
| filters | ||
| genotyper | ||
| haplotypecaller | ||
| indels | ||
| phasing | ||
| validation | ||
| varianteval | ||
| variantrecalibration | ||
| variantutils | ||