{"id":18246282,"url":"https://github.com/mfcovington/detect-boundaries","last_synced_at":"2025-04-08T19:26:07.073Z","repository":{"id":146346875,"uuid":"11066937","full_name":"mfcovington/detect-boundaries","owner":"mfcovington","description":null,"archived":false,"fork":false,"pushed_at":"2016-02-17T05:13:12.000Z","size":74,"stargazers_count":1,"open_issues_count":0,"forks_count":0,"subscribers_count":2,"default_branch":"develop","last_synced_at":"2025-02-14T15:15:33.400Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"Perl","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/mfcovington.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2013-06-30T09:09:01.000Z","updated_at":"2021-06-29T07:21:32.000Z","dependencies_parsed_at":"2023-05-03T06:46:44.028Z","dependency_job_id":null,"html_url":"https://github.com/mfcovington/detect-boundaries","commit_stats":null,"previous_names":[],"tags_count":9,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mfcovington%2Fdetect-boundaries","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mfcovington%2Fdetect-boundaries/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mfcovington%2Fdetect-boundaries/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mfcovington%2Fdetect-boundaries/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/mfcovington","download_url":"https://codeload.github.com/mfcovington/detect-boundaries/tar.gz/refs/heads/develop","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":247910679,"owners_count":21016734,"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":[],"created_at":"2024-11-05T09:25:16.121Z","updated_at":"2025-04-08T19:26:07.049Z","avatar_url":"https://github.com/mfcovington.png","language":"Perl","funding_links":[],"categories":[],"sub_categories":[],"readme":"\n\n\n`merge-replicates.pl`: Use if there are multiple replicates for a single sample and the genotype files need to be merged.\n\n- Input: Genotype files (one per chromosome per replicates for a sample)\n- Output: Merged genotype files (one per chromosome)\n\n`filter-snps.pl`: \n\n- Input:\n    - Sample ID\n    - Genotype files (one per chromosome for a sample)\n- Output: \n    - Boundaries file\n    - Filtered SNP files (one per chromosome)\n\n\n### Notes:\n\ndetect-boundaries:`filter-snps.pl`\n\n- IN:\n    - Genotyped files:\n- OUT:\n    - Boundary files: `sample-file/RIL_300.boundaries`, etc.\n    - Filtered SNP files: `RIL_300.A01.filtered.snps`, etc.\n\n\n### Merging Boundaries with `merge-boundaries.pl`\n\nThis script takes a collection of `*.boundaries` files and merges all of the boundaries. The bins resulting from the merge are written to a file: `bins.tsv`. Boundary and bin stats (count, min size, max size, and mean size) are printed to the screen.\n\nSample Usage:\n\n```shell\n./merge-boundaries.pl \\\n  --bam_file ~/git.repos/sample-files/bam/IMB211.good.bam \\\n  --chr_list A01,A02,A03,A04,A05,A06,A07,A08,A09,A10 \\\n  sample-file/RIL_*.boundaries\n```\n\n- IN:\n    - Boundary files: `sample-file/RIL_300.boundaries`, etc.\n    - Representative `.bam` file (for extracting chromosome lengths)\n    - (Optional) Chromosome list (for limiting analysis to a subset of sequences)\n- OUT: \n    - Comprehensive list of bins and their locations: `bins.tsv`\n\ndetect-boundaries:`extract-snp-subset.R`\n\n- IN:\n    - VCF summaries: `/Users/mfc/git.repos/snps-from-rils/merged.EC50.minflter.vcf/summaries.het_ratio_0_1.alt_ratmin_0_05.filters/merged.*.EC50.minflter.vcf.summary`\n    - Bins: `bins.tsv`\n- OUT: \n    - `sample-file/bins-snp.mid`\n\n\ndetect-boundaries:`get-genotypes-for-snp-subset.pl`\n\n- IN:\n    - `sample-file/bins-snp.mid`\n    - Genotyped files:\n    - polyDB...\n    - list of Sample IDs\n- OUT:\n    - `bin-genotype`\n\n*Version 0.6.0*\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmfcovington%2Fdetect-boundaries","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmfcovington%2Fdetect-boundaries","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmfcovington%2Fdetect-boundaries/lists"}