vcf2multialign

Create a set of reference-guided multiple-aligned haplotypes or founder sequences from a variant call file and a reference sequence. Please see releases for statically linked pre-built binaries (i.e. no dependencies) and Anaconda.org for dynamically linked ones.

Academic Use

If you use the software in an academic setting, we kindly ask you to cite Founder reconstruction enables scalable and seamless pangenomic analysis.

@article{Norri2021FounderReconstruction,
  title = {Founder reconstruction enables scalable and seamless pangenomic analysis},
  keywords = {READ ALIGNMENT, GENOMES, GRAPHS, SET, 113 Computer and information sciences},
  author = {Tuukka Norri and Bastien Cazaux and Saska D{\"o}nges and Daniel Valenzuela and Veli M{\"a}kinen},
  year = {2021},
  month = dec,
  day = {15},
  doi = {10.1093/bioinformatics/btab516},
  url = {https://doi.org/10.1093/bioinformatics/btab516},
  language = {English},
  volume = {37},
  pages = {4611--4619},
  journal = {Bioinformatics},
  issn = {1367-4803},
  publisher = {Oxford University Press},
  number = {24}
}

Building

To clone the repository with submodules, please use git clone --recursive https://github.com/tsnorri/vcf2multialign.git.

With conda-build

A conda package can be built with conda-build as follows. The build script has been tested with conda-build 3.27.0. glibc 2.28 or newer is required.

1. cd conda
2. ./conda-build.sh

By hand

The following software and libraries are required to build vcf2multialign. The tested versions are also listed.

• Reasonably new compilers for C and C++. We use GCC 12.3 in C++2b mode for our builds.
• GNU gengetopt 2.23
• Ragel State Machine Compiler 6.10
• Boost 1.82.0
• libbsd on Linux.

After installing the prerequisites, please do the following:

1. Create a file called local.mk in the root of the cloned repository to specify build variables. One of the files linux-static.local.mk and conda/local.mk.m4 may be used as a starting point.
2. Run Make with e.g. make -j16 dist to create a gzipped tar archive of the executables.

Usage

Outputting a reference-guided multiple sequence alignment of predicted haplotype sequences to haplotypes.a2m (similar to FASTA, with only uppercase characters). Sequence 1 from hs37d5.fa is used as the reference and the variants of the chr1 chromosome from variants.vcf as the variants:

vcf2multialign --haplotypes --input-reference=hs37d5.fa --reference-sequence=1 --input-variants=variants.vcf --output-sequences-a2m=founders.a2m --chromosome=chr1

Outputting a reference-guided multiple sequence alignment of 25 founder sequences to founders.a2m with a minimum aligned distance of 50 between the graph components using the same inputs:

vcf2multialign --founder-sequences=25 --minimum-distance=50 --input-reference=hs37d5.fa --reference-sequence=1 --input-variants=variants.vcf --output-sequences-a2m=founders.a2m --chromosome=chr1

Please refer to vcf2multialign --help for a complete list of options.