feat: add option to allow mapping to pangenome

snakemake-workflows / dna-seq-varlociraptor

A Snakemake workflow for calling small and structural variants under any kind of scenario (tumor/normal, tumor/normal/relapse, germline, pedigree, populations) via the unified statistical model of Varlociraptor.

MIT License

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feat: add option to allow mapping to pangenome #274

Open huzuner opened 10 months ago

huzuner commented 10 months ago

This PR allows an optional pangenome alignment with vg giraffe. The following additions/changes are made:

A new option pangenome is added to the config.
A rule to download the vg pangenome index is added into ref.smk.
Six other rules for aligning reads to the pangenome and preprocessing the resulting bam were added, into mapping.smk.
All input functions are updated to get pangenome aligned bam upon activation of pangenome in the config file.

huzuner commented 7 months ago

Bug with vg: alignments with deletions on ends: https://github.com/vgteam/vg/issues/4204. They fixed the issue and the new release is coming on Feb. 26.