{"id":13639295,"url":"https://github.com/brentp/excord","last_synced_at":"2025-06-30T12:34:33.434Z","repository":{"id":57692375,"uuid":"107149475","full_name":"brentp/excord","owner":"brentp","description":"extract SV signal from a BAM ","archived":false,"fork":false,"pushed_at":"2018-07-26T19:39:50.000Z","size":19,"stargazers_count":11,"open_issues_count":1,"forks_count":1,"subscribers_count":3,"default_branch":"master","last_synced_at":"2025-04-09T11:13:11.419Z","etag":null,"topics":["genomics","structural-variation"],"latest_commit_sha":null,"homepage":null,"language":"Go","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"apache-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/brentp.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}},"created_at":"2017-10-16T15:50:34.000Z","updated_at":"2022-11-02T14:58:14.000Z","dependencies_parsed_at":"2022-09-26T21:00:56.358Z","dependency_job_id":null,"html_url":"https://github.com/brentp/excord","commit_stats":null,"previous_names":[],"tags_count":3,"template":false,"template_full_name":null,"purl":"pkg:github/brentp/excord","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/brentp%2Fexcord","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/brentp%2Fexcord/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/brentp%2Fexcord/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/brentp%2Fexcord/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/brentp","download_url":"https://codeload.github.com/brentp/excord/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/brentp%2Fexcord/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":262774053,"owners_count":23362232,"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":["genomics","structural-variation"],"created_at":"2024-08-02T01:00:59.387Z","updated_at":"2025-06-30T12:34:33.381Z","avatar_url":"https://github.com/brentp.png","language":"Go","funding_links":[],"categories":["Variant Analysis and Manipulation"],"sub_categories":[],"readme":"# excord\n\nexcord extracts split and paired-end reads that are possible \nindicators of structural variation. It also outputs reference\ndepth.\n\nThe output of excord is used as input to [stix SV index](https://github.com/ryanlayer/stix)\n\n## usage\n\nBy default excord expects stuff from a single chromosome:\n```\nexcord --fasta $fasta --prefix some/cool/project $bam $chrom | bgzip -c \u003e $out\n```\nThis will write some/cool/project.rp.bin with reference and pair coverage interleaved.\n\nIt's possible to read a bam from stdin and write only the discorants and splitters:\n```\n\u003cbam stream\u003e | excord --discordantdistance 500 --fasta $fasta /dev/stdin | bgzip -c \u003e $out\n```\nIt's not possible to write reference coverage with this mode.\n\n\n## Ack\n\nexcord is developed as part of the company base2 genomics.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbrentp%2Fexcord","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbrentp%2Fexcord","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbrentp%2Fexcord/lists"}