v1.8.8

Improvements

Small precision increase, mainly for short-reads
Small sensitivity increase for long-reads
Added AF (allele-frequency) filter option to dysgu filter
Better allele-frequency estimation

Bug fixes

Re-mapping issue fixed (wrong site being chosen)
Clustering bug fixed affecting high-coverage regions
Other minor bug fixes

v1.8.7

Fixes

• #151 Fixes TypeError when working with phased bam

v1.8.6

Fixes

• #148 Migrate to superintervals >= 0.3
• #135 Partial fix for issue where ALT and REF bases are reported as the same. This occurred at complex SV sites in a polyploid genome. More events now undergo re-mapping resulting in better annotation of these loci and a reduction in the problem. A Warning is also now triggered if this issue occurs, and the SV will be annotated with symbolic notation to prevent issues with downstream tools.

v1.8.5

Improvements

• QUAL field is now added to output #140

Bug fixes

• Fix for malformed HP tag #136 #144
• Symbolic SV option is now respected for paired-end reads
• Fixed typos in CLI help menu

v1.8.4

Improvements

• Switched to meson build system for much faster build times

Bug fixes

• Phase set tag PSET changed to integer value
• #136 Malformed VCF after merging now fixed
• #144 Large INV missing FCC value

v1.8.3

Bug fixes

This release fixes the following issues

• #135 Missing REF allele sequences for some calls
• #136 Merging using dysgu 1.8 and older VCF versions

v1.8.2

Improvements

• Slightly better performance for paired-end reads

Minor bug fixes

• Remove unnecessary check for sorted bam file #129 @Lupphes
• Fixed out-by-one bug since v1.8.1 fetching an extra base for deletion sequence events

v1.8.1

Bug fixes

• Fixed zero division error
• #125, missing call when support is low
• Reference base issue causing issues with IGV

v1.8.0

Improvements

• SV phasing is now supported. Supply dysgu with a 'haplotagged' bam file (with HP and PS tags for reads) and dysgu will automatically phase output SVs. This results in a large increase in performance for long reads (see PacBio benchmark here: https://github.com/kcleal/SV_Benchmark_CMRG_GIAB)
• Added AF allele frequency to FORMAT column #117
• New progressive merge method when using dysgu merge that allows better scaling to large cohorts. This can be set using --merge-method [ auto | all-vs-all | progressive ], default is auto #82
• Improvements to merging SVs during calling

Fixes

• Fixed DUP sequences ending up in REF column #123

v1.7.0

v1.7.0

This release brings important improvements:

• Much improved sensitivity, especially for long-read data at multi-allelic sites, or clustered SVs on the same haplotype
• Faster runtime
• New preset modes for pacbio-revio and nanopore-r10

Issues fixed:

• Overriding presets works as expected
• #114, #109

CLI changes:

• --no-gt flag has been removed
• --mode pacbio and --mode nanopore presets have been changed to --mode pacbio-sequel2 and --mode nanopore-r9
• Using run pipeline with long-reads (cram files) now applies compression to the temp bam file wb3