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

v1.6.7

Minor release

Fixes for the following issues:

#107
#90

v1.6.6

Minor release

Addresses the following issues with dysgu filter command:

• Fixes a regression bug which caused dysgu filter to drop intra-chromosomal SVs for paired-end reads #100
• Fixes #99 --keep-all now works for dysgu filter @kdm9
• Fixes a zero division error for long-reads using dysgu filter

v1.6.5

v1.6.5

Minor update adding following features and fixes

• Faster --cohort-update option for dysgu merge
• Returns an empty vcf file (with header) when no events called
• Merged #89 thanks to @JMencius checks for sorted input where possible
• Small speed increase

v1.6.3

New features

• More options to tune sensitivity using --sd (span-distance, used for insertion clustering) and --search-depth options
• Ability to filter on mapq when using dysgu-filter
• --cohort-update option for dysgu merge, allowing regenotyped calls to be updated in a cohort file
• More efficient merging of large cohorts - option for limiting number of local SV comparisons using dysgu-merge via --max-comparisons
• Improved somatic filtering
• Slightly improved runtime and memory footprint
• Support for python 3.12
• --verbose option for dysgu test
• Added MAPQS to format line (mapq supplementary-reads)
• Added NMB to format line (Edit distance, ignoring large gaps and soft-clips)

Bug Fixes

• Missing usage of bam file tell when using dysgu-call (improves sensitivity slightly)
• Minor clustering bug (improves sensitivity slightly)
• #81 #83

v1.6.2

Minor release

• Added option to use a file list for filtering normals using dysgu filter input.vcf list_of_normals.txt > output.vcf
• Bug fix: using -o option with a / in file name, and combined with bam file stdin, now works again

v1.6.1

Improvements / changes

• Added --symbolic-sv-size option to switch between symbolic or sequence representation
• Added parallel processing for merge command
• Added --ignore-sample-sites option to ignore the input sample when using --sites. This is set at True by default and addresses #37
• Minimum python version now 3.8

Bug fixes

• Fixed #69 #70
• Fixed minor issue resulting in dropping of paired-end INS SVs

v1.6.0

Improvements / changes

• Added 'auto' option for setting --min-support, this is set as default for long-reads
• Long-reads default mapq lowered to 1
• Improved sensitivity for large-insertions using long-reads
• Small numbers of BND events also now reported for long-reads
• Improved precision due to better SV merging and lower numbers of duplicated true-positive calls
• Coverage values now include reads < mapq threshold
• Around 10 % of insertions are now re-classified as DUP; occurs when split-read support is available

Bug fixes

• Segfault for high coverage sample
• Exponential runtime for very large component in graph

v1.5.0

v1.5.0

• Significantly improved precision for long read SV calling
• Long-reads with poorly mapped ends are now ignored, controlled using --divergence option
• Nearby indels on the same read are now merged, controlled the --length-extend option
• CLI change: filter-normal command has been renamed filter and supports more options for filtering
• Improvements in runtime for long-reads