Full Changelog: https://github.com/fritzsedlazeck/Sniffles/compare/v2.3.3...v2.4

Bugfixes to make sure sniffles shuts down properly.

Full Changelog: https://github.com/fritzsedlazeck/Sniffles/compare/v2.3.2...v2.3.3

manage the Sniffles2Exit exception in order to not have --version and --help trowing an exit code 1 which made conda not accept sniffles v2.3.1

Full Changelog: https://github.com/fritzsedlazeck/Sniffles/compare/v2.3.1...v2.3.2

Bug fixes that prevented pip installation to work and thus conda was unable to build and release
Full Changelog: https://github.com/fritzsedlazeck/Sniffles/compare/v2.3...v2.3.1

This release includes new features for multisample calling and some restructuring of the codebase to facilitate easier development in the future.

New features:

• Multisample calling for large input sets
  Sniffles multiprocessing code has undergone a major rewrite with focus of enabling multisample calling for a large number of input files. To support this, the new optional dependency psutil can be installed along with sniffles.

• Using alignments for multisample calling
  Alignments can be used to improve separation of variants in multisample calling. This uses the new optional dependency edlib and can be tweaked with the new argument --combine-pctseq defaulting to 0.7.

Required Python version has been updated to Python 3.10.

This release includes a number of updated implementation, bug fixes and usability improvements.

• Low frequency SV caller mode --non-germline has been updated to --mosaic
• Sniffles now allow SV on the same breakpoint
• Minimum SV length is updated to 50 bases
• Minimum mapping quality is set to 20 as default
• Translocation events: require a minimum anchor on each chromosome of 1kb and there a strand check (--bnd-min-split-length and --qc-bnd-filter-strand)
• We include a link to a Sniffles2 plotting tools: https://github.com/farhangus/sniffle2_plot

This release includes a number of minor bugfixes and usability improvements.

• Create output directories if they are not existing yet (@wdecoster)
• Change --max-splits-kb to float (@wdecoster)
• Fixed a problem where exit code 0 was returned on errors

In comparison to 2.0.2 a number of improvements to multi-sample mode were added:

• Improved choice of insertion sequence for reporting
• Added additional INFO fields to multi-sample output
• Fixed a problem causing inconsistent start/end coordinates for deletions
• Increased strictness of default merging parameters

This is a major update to Sniffles v2 which includes:

• Improved variant calling accuracy
• Improved performance also on multi threading
• New methods to enable family / population calling
• New methods to enable somatic / mosaic SV detection

Multiple improvements including:
-) Genotype prediction
-) Report of strand biases per allele
-) Higher sensitivity on low supported alleles
-) Improved forced calling

• Improved reporting of sequence resolved calls.
• Minor bug fixes.

• Changed SVlen for deletions (new VCF standard)
• Changed BND output
• Improvements on genotyping for forced calling

• Added functionality to call multisample genotyped SVs VCF file by interacting with SURVIVOR.
• Bug fixes for reporting sequences and force calling
• Added new interface for clearer navigation.

Sniffles:

• Added sequence resolved calls.
• Changed -n parameter (-n -1) reports now all read names.

Parameter added

--report_seq : Reports the sequences of Indels in the VCF output
--min_homo_af: Adapt the threshold to infer a homozygous variant
--min_het_af: Adapt the threshold to infer a heterozygous variant
--Ivcf: Enabling Recalling/force calling given a VCF file.

Bug fixes

• Bugs corrected in genotype estimation
• BND flag

Fixes

• Avoid calling SV in N stretches of certain sizes .
• Included genome header in vcf and BND type support.

Fixes

• More constrained calling of InvDup.
• Increased sensitivity for small indels.

Extension

• Parameter introduced: --ignore_std disable the filtering based on std.

Fixes

• Seg. fault sometimes occurring at the end of the run
• Enhanced resolution for smaller indel in noisy regions
• Constrained calling of INVDUP

Extention

• Parameter introduced: Min segment length

New features:

1. Automatic distance computation
2. STD computations and filtering of breakpoints to detect artifacts
3. Detection of small translocated elements
4. New SV type
5. Enhanced small indel calling

Bug Fixes:

1. Merging of SVs within the tree

Reduce false calls over using nanopore reads.
Changes in the VCF file to support IGV display for translocations.