SVIM v2.0.0

Stable release 2.0.0

Changelog:

• adds consensus sequence computation for insertions
• improves clustering step:
  • considers sequence similarity when clustering insertions
  • prevents signatures from same read to be clustered together
• outputs sequence alleles for all SV types except BNDs and DUPs by default
• updates default parameters
• bugfixes

SVIM v2.0.0-beta.1

Beta release 2.0.0

Changelog:

• adds consensus sequence computation for insertions
• improves clustering step:
  • considers sequence similarity when clustering insertions
  • prevents signatures from same read to be clustered together
• outputs sequence alleles for all SV types except BNDs and DUPs by default
• updates default parameters
• bugfixes

SVIM v1.4.2

Stable release 1.4.2

Changelog:

• fix invalid start coordinates in VCF output
• issue warning for invalid characters in contig names

SVIM v1.4.1

Stable release 1.4.1

Changelog:

• improve clustering of translocation breakpoints (BNDs)
• improve --all_bnds mode
• bugfixes

SVIM v1.4.0

Stable release 1.4.0

Changelog:

• fix and improve clustering of insertions (fix bugs introduced in v1.3.1)
• add option --all_bnds to output all SV classes in breakend notation
• update default value of --partition_max_distance to avoid very large partitions
• various bugfixes

SVIM v1.3.1

Stable release 1.3.1

Changelog:

• Small changes to partitioning and clustering algorithm
• Add two new command-line options to output duplications as INS records in VCF
• Remove limit on number of supplementary alignments
• Remove q5 filter
• Bugfixes

SVIM v1.3.0

Stable release 1.3.0

Changelog:

• Improve BND detection by detecting BNDs connecting opposite strands
• Add INFO:ZMWS tag to output VCF with number of supporting PacBio wells (enables filtering bad calls from only a few ZMWs)
• Add sequence alleles for INS (using the insertion sequence from a random supporting read)
• Add FORMAT:CN tag for tandem duplications
• Bugfixes

SVIM v1.2.0

Stable release 1.2.0

Changelog:

• add option --sequence_alleles to output sequence instead of symbolic alleles in VCF
• add option --insertion_sequences to output insertion sequences in VCF
• add option --read_names to output names of supporting reads in VCF

SVIM v1.1.1

Stable release 1.1.1

Changelog:

• Output breakends (BND) in VCF file
• Detect large tandem duplications even if they are not spanned by a single read (add flag not_fully_covered)
• Add new command line option to skip genotyping
• Make VCF output more flexible:
  • Let user choose which SV types to include in VCF output
  • Let user choose how to represent tandem and interspersed duplications (either as DUP or as INS)
• Add scatter plot of read support for reference and variant allele (see below)

SVIM v1.0.0

Stable release 1.0.0

Changelog:

• Add genotyping of deletions, inversions, insertions and interspersed duplications
• Improve help descriptions
• Produce plots of SV length distribution (see below)