v2.0.2

Minor patch to fix PS tags when haplotagged reads aren't provided.

Full Changelog: v2.0.1...v2.0.2

v2.0.1

Minor patch of the dependencies so that bioconda can build/distribute.

Full Changelog: v2.0.0...v2.0.1

v2.0.0

Expanded joint genotyping capabilities and enhanced flexibility for structural variant analysis.

New Features

Joint Genotyping Modes

• Added kanpig trio command for joint genotyping of structural variants in parent-child trios
• Added kanpig mosaic command for joint genotyping of low variant allele frequency (VAF) structural variants

Enhanced Input/Output Options

• BAM/CRAM files can now be read directly from remote URLs
• Symbolic deletion notation (<DEL>) is now supported
• New optional --rnames flag outputs SVID and supporting read names (requires BAM --reads input)
• Optional genotype quality (GQ) calibration now available (see gqcalibration/README.md for details)

Python API

Python-Rust bindings now expose plup parsing, kmer vectorization, and genotyper math functionality for custom scripting

Improvements

• Refined mathematical calculations for more informative genotype quality scores and improved genotype calls
• VCF outputs now include a comment line with kanpig version and command information for better reproducibility
• Significant code refactoring to improve reusability and facilitate creation of new sub-commands
• Established functional testing infrastructure in repo_utils/

Changes

• Removed FORMAT/NE field from output. When phase set (PS) tags are not available from BAM/plup files, the neighborhood ID for short-range phase groups now defaults to the 1-based start position of the upstream-most SV in the neighborhood

Full Updates: https://github.com/ACEnglish/kanpig/wiki/Updates#v200
Full Changelog: v1.1.0...v2.0.0

v1.1.0

• New --ab allele balance threshold lowers frequency of assigning erroneous compound heterozygous genotypes
• Experimental --squish changes gpenalty behavior to preferring simpler paths
• Fix score's gpenalty
• FORMAT/NE now uses neighborhood's start position for consistent labeling across samples

Full Changelog: v1.0.2...v1.1.0

v1.0.2

Minor patch

• UI tweaks, including cleaner gt parameters
• Slight htslib bam record and other minor efficiency improvement
• Fix bug arising from ploidy==1 regions sometimes.
• Fix minor bugs around PS and HP tag counting/record keeping

Full Changelog: v1.0.1...v1.0.2

v1.0.1

Faster, Smaller, More Accurate Genotyping

Kanpig now has sub-commands gt and plup. The new plup command will extract reads and their SVs from a bam file into a small file that's useful for long-term storage of reads.

• gt improvements:
  • can parse plup files much more quickly (up to 8x) than parsing a bam. Though bam parsing is also now ~2x faster.
  • parse PS and HP information from haplotagged reads to increase genotyping accuracy as well as record long-range phasing information in the output VCF.
  • now uses kmedoid clustering instead of kmeans, resulting in a modest improvement to genotyping accuracy.

Full Updates: https://github.com/ACEnglish/kanpig/wiki/Updates#v101
Full Changelog: v0.3.1...v1.0.1

v0.3.1

Consistency improvements

• New filtering of haplotypes without paths increases accuracy
• New path scoring improves accuracy and consistency
• ZS and SS FORMAT fields replaced by KS reporting the score
• Requiring reads to span the full variant graph window including --chunksize buffer increases accuracy
• Exhaustive search of partial haplotypes
• Slight runtime reduction from avoidance of redundant path searches

Full Changelog: v0.3.0...v0.3.1

v0.3.0

General improvements

• ~8% speed increase from less work in the path-searching
• Partial haplotypes bug fix increases accuracy
• Fixed SQ and FT fields
• Dedicated writing thread helps reduce memory usage by preventing a backlog of completed variants while reading
• Default --out is stdout to allow easier compression/indexing (e.g. kanpig .. | bcftools sort -O z -o out.vcf.gz)
• IUPAC codes are fixed by kanpig according to vcf specifications (Issue #1)
• Fixed filtering of symbolic alts and BNDs
• Argument validation

Full Changelog: v0.2.0...v0.3.0

v0.2.0

• Up to 40% reduction in runtime
• Hemizygous and sex chromosome aware genotyping with new --ploidy-bed
• Variants with alternate alleles of stars, monozygotic reference, and BNDs are filtered out
• Comparing PathScores by their average size and sequence similarity increases accuracy

Full Changelog: v0.1.2...v0.2.0

v0.1.2

• New optional hompolymer filter doesn't kmerize long homopolymers
• Improved logging info
• Correcting GQ field
• Correcting kmer counting
• Small speed/memory/io improvements
  • Off-loaded annotation work from the single writer thread to the worker threads and using a large
    multiple of page size for the BufWriter capacity
  • Fewer bam file opens
  • Fewer clone operations

Full Changelog: v0.1.0...v0.1.2