Major Changes:
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Introducing GeminiMulti as a mate-aware indel realigner. This combines the best of Hygea (realigner) and Stitcher (the read stitcher), using a read's mate to inform realignment (if a mate is available). With no mate, it falls back to just doing indel realignment. Gemini is also smoking fast. Gwenn Berry is the lead developer for Gemini. Note that Gemini is very new, and may be hardened/refactored in future releases. When using Gemini with Pisces, please set -UseStitchedXD true.
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Introducing AdaptiveGenotyper as a new alternative to the simplistic threshold-based germline genotyping model originally in Pisces. To use AdaptiveGenotyper, take a normal BAM from a germline sample. Call with Pisces in somatic, uncrushed VCF mode (in order to report all alleles present, including noise). AdaptiveGenotyper will then adaptively build up three-component (or four-component) binomial mixture models as appropriate for a diploid sample, and re-genotype based on those models. Sidney Kuo is the lead developer for the AdaptiveGenotyper. Note that AdaptiveGenotyper is very new, and may be hardened/refactored in future releases.
Minor Fixes:
- VennVcf is no longer so finicky about chr names.
- Pisces allows non-anchored indels