Pisces Release Notes (official builds)
Somatic Calling
- Improve somatic accuracy by improving Q scores accuracy
Germline Calling
- Update for compatibility with diploid phasing
- Clean up overlapping variants into two separate alleles, as MNVs
- Accurate functional consequence through complex regions
- Location merging for not-co-located 1/2 GT
- Genotype reporting at loci inside deletions and MNVs reported at earlier loci
Filtering
- Allow application of RMxN filter to depend on variant frequency
Usability and Performance
- Remove depracated aliases for command line options and make input arguments case insensitive
- Update default value for Collapse parameter to true
- Remove GTModel parameter
- If supplied output folder doesn't exist, be kind to the user and create it
- Remove internal stitching in favor of separate read-stitching executable
- Turn off interval jumping during BAM reading
Bug Fixes
- Some references were getting a PASS when they failed Q-score but did not fail depth (rare case, when a deletion or MNV would eat up all the other coverage, so coverage was high, but ref support was low enough to flunk Q score)
- Fix bug in rounding when calculating coverage/variant frequency over a spanning stitched variant
- Fix germline location merging for indels
The Stitcher reconciles paired alignments in a supplied BAM file, outputting a "stitched" BAM where each valid overlapping pair is merged into a single read. This allows for more accurate, fragment-based representation of paired end data - both in terms of coverage and of base-calling/alignment confidence by addressing agreements and disagreements in overlapping regions of paired reads.
Details at: Stitcher-5.1.6-Design-Document
Detects multiple nucleotide variants (MNVs) in a given sample and phases the variants in complex regions into sub populations. Allows phasing of variants across reads.
Details at: Scylla-5.1.6-Design-Document
Recalibrates the variant quality scores (Q scores) if the particular variants are over represented
Details at: VQR-5.1.6-Design-Document
- Pisces 5.2.10 Design Document
- Pisces 5.2.10 Supported Options
- Scylla 5.2.10 Design Document
- Stitcher 5.2.10 Design Document
- VQR 5.2.10 Design Document
- VennVcf 5.2.10 Design Document
- Gemini 5.2.10 Design Document
- AdaptiveGenotyper 5.2.10 Design Document
- Pisces Tools 5.2.10
- Suggested Pipeline Configuration 5.2.10
- Pisces 5.2.9 Quick Start
- Pisces 5.2.9 Design Document
- Pisces 5.2.9 Supported Options
- Scylla 5.2.9 Design Document
- Stitcher 5.2.9 Design Document
- VQR 5.2.9 Design Document
- VennVcf 5.2.9 Design Document
- Pisces Tools 5.2.9
- Suggested Pipeline Configuration 5.2.9
- Pisces 5.2.7 Quick Start
- Pisces 5.2.7 Design Document
- Pisces 5.2.7 Supported Options
- Scylla 5.2.7 Design Document
- Stitcher 5.2.7 Design Document
- VQR 5.2.7 Design Document
- VennVcf 5.2.7 Design Document
- Pisces Tools 5.2.7
- Suggested Pipeline Configuration 5.2.7
- Pisces 5.2.5 Design Document
- Pisces 5.2.5 Supported Options
- Scylla 5.2.5 Design Document
- Stitcher 5.2.5 Design Document
- VQR 5.2.5 Design Document
- Suggested Pipeline Configuration 5.2.5
- Pisces 5.2.0 Design Document
- Pisces 5.2.0 Supported Options
- Scylla 5.2.0 Design Document
- Stitcher 5.2.0 Design Document
- VQR 5.2.0 Design Document
- Suggested Pipeline Configuration 5.2.0
- Pisces Suite 5.2.0 Known Issues and Limitations