Variant calling comparisons across vg giraffe versions

This repository is a fork of long-read-giraffe-experiments. To make this one easier to use, it has strictly less functionality and will only let you compare variant calling results between vg giraffe versions. If you only need read alignment comparisons, please check out the giraffe-parameter-search repo.

Note that this repository assumes that all graphs & indexes will already exist. All of the machinery to index graphs or perform haplotype sampling etc. has been removed.

Set up this repository in /private/groups. The pipeline will create very large files (e.g. read alignments) which will not fit within /private/home directories.

Usage

The general flow for using this repository is:

1. Get static vg binaries for the versions you want to compare. For each, navigate to inside your vg installation folder.

   1. git checkout the branch (e.g. git checkout mybranch) or commit hash (e.g. git checkout e2547e979d86a446e8151c5489850b6176a82c0c)
   2. Note the first six characters of the commit hash. If you don't know them, run git rev-parse HEAD.
   3. Make a static binary with:

      make -j32 static
      strip -d bin/vg
      ```

   4. Copy the binary file to inside this directory, where COMMIT is replaced by the six-character commit hash:

      # For example; replace with where this directory is
      VC_TEST_REPO=/private/groups/patenlab/$USER/giraffe-variant-calling-tests
      cp bin/vg $VC_TEST_REPO/vg_COMMIT
      

2. Update the compare_variant_calling experiment by replacing the commit hashes (hifi-COMMIT-noflags & r10-COMMIT-noflags) with the six-character hashes of your binaries. There should be one hifi and one r10 version for each of the commits you're testing. Make sure the constrain section has the hifi versions for hifi reads, and visa versa.

3. Run the Snakefile (invoke from right inside this folder)

   (umask 002 && snakemake -j128 --rerun-incomplete --use-singularity --singularity-args "-B /private" --latency-wait 120 --executor slurm --keep-going ./output/experiments/compare_variant_calling/plots/{snp,indel,total}_errors.png)
   

Please note that the vg surject invocation will be done by whichever vg is on your PATH, not by the vg which did the read alignment. The specialized versions are used only for giraffe.

Dependencies

The following conda environment was sufficient to run vg version comparison variant calling tests on the Phoenix cluster:

conda create -n vc-compare -c conda-forge -c bioconda snakemake=9.13.7 \
    toil snakemake-executor-plugin-slurm snakemake-storage-plugin-http singularity \
    bidict matplotlib meryl 'minimap2>=2.28' seqkit