Version 2.7.7

Download release

Linux 64bit binary

The binary is statically linked for linux 64bit and should run without installing the dependencies. Before running the binary you should enable executable permissions

wget https://github.com/DecodeGenetics/graphtyper/releases/download/v2.7.7/graphtyper
chmod a+x graphtyper

Release notes

• Added calculation of excess heterozygosity P-value (INFO/PexcessHet).
• Several minor fixes in snp/indel calling.

Version 2.7.6

Download release

Linux 64bit binary

The binary is statically linked for linux 64bit and should run without installing the dependencies. Before running the binary you should enable executable permissions

wget https://github.com/DecodeGenetics/graphtyper/releases/download/v2.7.6/graphtyper
chmod a+x graphtyper

Release notes

• Support for ARM64 (thanks to @martin-g )
• Fix for rare bug in discovery.
• Improvements for encoding popVCFs.
• Support for DRAGEN SV VCFs

Version 2.7.5

Download release

Linux 64bit binary

The binary is statically linked for linux 64bit and should run without installing the dependencies. Before running the binary you should enable executable permissions

wget https://github.com/DecodeGenetics/graphtyper/releases/download/v2.7.5/graphtyper
chmod a+x graphtyper

Release notes

Bug fix in alignment code.

Version 2.7.4

Download release

Linux 64bit binary

The binary is statically linked for linux 64bit and should run without installing the dependencies. Before running the binary you should enable executable permissions

wget https://github.com/DecodeGenetics/graphtyper/releases/download/v2.7.4/graphtyper
chmod a+x graphtyper

Release notes

Enhancements:

• Added binning of PL values.
• Added popVCF encoding, use the "--encoding=popvcf" to enable. See: https://github.com/DecodeGenetics/popvcf

Version 2.7.3

Download release

Linux 64bit binary

The binary is statically linked for linux 64bit and should run without installing the dependencies. Before running the binary you should enable executable permissions

wget https://github.com/DecodeGenetics/graphtyper/releases/download/v2.7.3/graphtyper
chmod a+x graphtyper

Release notes

Bug fixes:

• Fixed a rare segfault in genotype_hla.

Enhancements:

• Added a check for VCF records that may exceed the 2GB limit of htslib. Currently, these records will be omitted but we are working on providing a better workaround.
• Updated the paw submodule.
• Not filtering out zero quality SVs is now the default behavior, since it is needed in population calling which is likely the most common use case. The old behavior can be obtained with the --force_filter_zero_qual option.

Version 2.7.2

Download release

Linux 64bit binary

The binary is statically linked for linux 64bit and should run without installing the dependencies. Before running the binary you should enable executable permissions

wget https://github.com/DecodeGenetics/graphtyper/releases/download/v2.7.2/graphtyper
chmod a+x graphtyper

Release notes

Bug fixes:

• Fixed a rare bug in genotype related to IUPAC bases (#78).

Enhancements:

• Added new option --uncompressed_sample_names which ensures that the sample names are in 0-compressed bgzf blocks.
• Several speed improvements, i.e. replaced std::map/unordered_map with parallel hashmap counterparts.
• Removes Boost dependency. Boost.Serialization was replaced with Cereal. Note that any serialized graphs are not compatible between Boost.Serialization and Cereal so those will need to be reconstructed.
• Moved from Travis CI to Github actions.
• Improvements in 4-digit HLA genotyping. With these changes, when too many 4-digit HLA types are found in the population then they the most infrequent ones are merged.
• clang-format and clang-tidy configs added.
• Removal of all system() calls.
• Optimization of work is split between threads.
• C++ standard changed from C++11 to C++17. We therefore require a compiler that supports C++17 and compiles AVX512 code (GCC 7+ or Clang 10+). Note that these compilers is not required for running the graphtyper static binary.
• Reworked how phase information is stored in initial discovery step to greatly reduce memory usage of that step.

Version 2.7.1

Download release

Linux 64bit binary

The binary is statically linked for linux 64bit and should run without installing the dependencies. Before running the binary you should enable executable permissions

wget https://github.com/DecodeGenetics/graphtyper/releases/download/v2.7.1/graphtyper
chmod a+x graphtyper

Release notes

• Full AVX512 support. The extention set is checked at runtime and will be automatically utilized on system that have it.
• Added new experimental subcommand "genotype_hla" for MHC/HLA genotyping (detailed instruction on how to run this will be added to the wiki).
• Removed a parameter setting which had poor performance on very diverse populations.
• Small variant discovery algorithm mode reworked.
• Several other minor bugfixes and improvements in small variant calling.

Version 2.6.2

Download release

Linux 64bit binary

The binary is statically linked for linux 64bit and should run without installing the dependencies. Before running the binary you should enable executable permissions

wget https://github.com/DecodeGenetics/graphtyper/releases/download/v2.6.2/graphtyper
chmod a+x graphtyper

Release notes

• Fixed a rare memory segfault when running with CRAI files in genotype_sv.

Version 2.6.1

Download release

Linux 64bit binary

The binary is statically linked for linux 64bit and should run without installing the dependencies. Before running the binary you should enable executable permissions

wget https://github.com/DecodeGenetics/graphtyper/releases/download/v2.6.1/graphtyper
chmod a+x graphtyper

Release notes

• Added option for extra call_only iteration. Added check for duplicated sample names.
• Added coverage filter in the 'genotype_sv' subcommand. It is possible to turn the filter off with a new '--no_filter_on_coverage' command.
• Another fix for a very rare bug in graph construction. Only affects very large-scale genotyping runs. WIP streamlined discovery.
• Write CSI instead of TBI with the --csi option.
• Added several per alt QC metrics to VCF output when calling genotype
• optimization for vcf_merge
• Added no_variant_overlapping option in force calling mode
• updated how QD and QDalt are calculated
• AAScore added in SNP/indel genotyping
• bugfix: In very large genotyping runs some INFO fields can get larger than INT_MAX so I needed to change them to be strings instead, otherwise bcftools is not happy with me.
• Added read subsampling in the genotype_sv subcommand if the option --avg_cov_by_readlen is set.
• License changed to MIT.

Version 2.5.1

Download release

Linux 64bit binary

The binary is statically linked for linux 64bit and should run without installing the dependencies. Before running the binary you should enable executable permissions

wget https://github.com/DecodeGenetics/graphtyper/releases/download/v2.5.1/graphtyper
chmod a+x graphtyper

Release notes

This is a bugfix release

• Bugfix in some rare sv graph construction
• Bugfix in some rare VCF merging cases
• Made failed copy of tabix index a warning in genotype_sv instead of error