{"id":19434643,"url":"https://github.com/edawson/svaha","last_synced_at":"2025-04-24T20:32:16.672Z","repository":{"id":150736396,"uuid":"65667614","full_name":"edawson/svaha","owner":"edawson","description":"Convert structural variants to sequence graphs [ VCF + FASTA ---\u003e GFA ]","archived":false,"fork":false,"pushed_at":"2024-03-06T15:32:03.000Z","size":11105,"stargazers_count":12,"open_issues_count":5,"forks_count":1,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-04-03T10:38:05.116Z","etag":null,"topics":["gfa","graph","variation-graph","vcf"],"latest_commit_sha":null,"homepage":null,"language":"C++","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/edawson.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2016-08-14T13:30:17.000Z","updated_at":"2025-02-06T21:11:49.000Z","dependencies_parsed_at":"2023-04-12T13:24:41.522Z","dependency_job_id":null,"html_url":"https://github.com/edawson/svaha","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/edawson%2Fsvaha","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/edawson%2Fsvaha/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/edawson%2Fsvaha/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/edawson%2Fsvaha/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/edawson","download_url":"https://codeload.github.com/edawson/svaha/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":250704863,"owners_count":21473775,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["gfa","graph","variation-graph","vcf"],"created_at":"2024-11-10T14:47:05.075Z","updated_at":"2025-04-24T20:32:16.667Z","avatar_url":"https://github.com/edawson.png","language":"C++","funding_links":[],"categories":[],"sub_categories":[],"readme":"svaha - generate variation graphs for structural variants.\n-----------\nMake variation graphs from structural variants:  \n[x] Deletions\n[x] Inversions\n[x] Insertions\n[x] SNPs\n[ ] Duplications\n[ ] Transversions\n[ ] Breakpoints\n\n\nDon't worry: we'll be adding these as time permits.  \n\n\n## What is svaha?\nsvaha is a small program that converts Variant Call Format (VCF) records into [Graphical Fragment Assembly](https://github.com/pmelsted/GFA-spec) format (i.e. sequence graphs like those in [vg](https://github.com/vgteam/vg)). It does so using a minimal single-base graph representation, the world's smallest and least-safe VCF parser (well, probably), and almost no dependencies.\n\n## Build it\nsvaha brings in its own libraries, except for zlib. Make sure to have zlib installed.\nIt uses a frozen version of htslib and floating versions of gfakluge. To build svaha:  \n\n                git clone --recursive https://github.com/edawson/svaha\n                make\n\n\nand that should do it.\n\n## Run svaha\nsvaha takes a FASTA file and a VCF as arguments:  \n        ```./svaha -r MYFASTA.fa -v MYVARIATION.vcf```\n\nand outputs sorted GFA, which is text-based and easily exchangeable to other, more useful programs (like vg).\n\n\n## Options\n`-r`: a fasta reference  \n`-v`: a vcf containing variants (must be relative to the given fasta)  \n`-m`: maximum node size. When creating graphs for vg, make sure to use a maximum node size of between 32 and 1023.  \n1023 is a hard limit (nothing 1024 or over will be indexable) and below 32 the graph begins to eat tons of memory. I tend to use `-m 64` or `-m 128`.\n\n## Workflows\n\n1. Build a variation graph with svaha containing structural variants  \n2. Reduce node size with a ``cat result.gfa | vg view -F -v - | vg mod -X 1000 - \u003e new_graph.vg`` to make the resulting graph indexable with GCSA2.  \n3. Map reads to that graph using ```vg map``` \n4. Call variants using ```vg call``` or ```vg genotype```\n\n\n## Get help\nReach out to me (@edawson) on GitHub and I'll do my best to help!\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fedawson%2Fsvaha","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fedawson%2Fsvaha","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fedawson%2Fsvaha/lists"}