{"id":47790909,"url":"https://github.com/oicr-gsi/delly","last_synced_at":"2026-04-03T15:37:46.511Z","repository":{"id":34790972,"uuid":"38774854","full_name":"oicr-gsi/delly","owner":"oicr-gsi","description":"Delly workflow produces a set of vcf files with different types of structural variant calls","archived":false,"fork":false,"pushed_at":"2026-01-13T02:15:53.000Z","size":336,"stargazers_count":1,"open_issues_count":0,"forks_count":2,"subscribers_count":8,"default_branch":"master","last_synced_at":"2026-01-13T05:50:44.782Z","etag":null,"topics":["structural-variation","variant-calling","workflow"],"latest_commit_sha":null,"homepage":"","language":"WDL","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/oicr-gsi.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG.md","contributing":null,"funding":null,"license":null,"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,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2015-07-08T19:20:28.000Z","updated_at":"2025-09-09T13:35:58.000Z","dependencies_parsed_at":"2025-05-26T21:23:24.098Z","dependency_job_id":"cf19bcb4-9e1d-4877-97e4-fb8743849703","html_url":"https://github.com/oicr-gsi/delly","commit_stats":null,"previous_names":[],"tags_count":12,"template":false,"template_full_name":null,"purl":"pkg:github/oicr-gsi/delly","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/oicr-gsi%2Fdelly","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/oicr-gsi%2Fdelly/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/oicr-gsi%2Fdelly/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/oicr-gsi%2Fdelly/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/oicr-gsi","download_url":"https://codeload.github.com/oicr-gsi/delly/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/oicr-gsi%2Fdelly/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":31360807,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-04-03T15:19:21.178Z","status":"ssl_error","status_checked_at":"2026-04-03T15:19:20.670Z","response_time":107,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.6:443 state=error: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"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":["structural-variation","variant-calling","workflow"],"created_at":"2026-04-03T15:37:45.829Z","updated_at":"2026-04-03T15:37:46.503Z","avatar_url":"https://github.com/oicr-gsi.png","language":"WDL","funding_links":[],"categories":[],"sub_categories":[],"readme":"# delly\n\nThe Delly workflow produces a set of vcf files with different types of structural variant calls: Translocations, Deletions, Inversions and Duplications It uses .bam files as input. The below graph describes the process:\n![delly flowchart](docs/delly-wf.png)\n### Preprocessing\nThe expected inputs for the DELLY tool are aligned sequence (bam format), properly sorted and indexed, with marked duplicates. \n### Mark duplicates\nPicard Tools MarkDuplicates is used to flag reads as PCR or optical duplicates and is activated by default.  If providing bam files with duplicates marked, this can be disabled.\n```\n java -jar MarkDuplicates.jar\n INPUT=sample.bam\n OUTPUT=sample.dedup.bam    \n METRICS_FILE=sample.metrics\n```\n### Detect deletions\n```\ndelly\n-t DEL\n-x excludeList.tsv\n-o sample.jumpy.bam\n-q 0\n-g hn19.fa\nsample.bam\n```\n### Detect tandem duplications\n```\ndelly\n-t DUP\n-x excludeList.tsv\n-o sample.jumpy.bam\n-q 0\n-g hn19.fa\nsample.bam\n```\n### Detect inversions\n```\ndelly\n-t INV\n-x excludeList.tsv\n-o sample.jumpy.bam\n-q 0\n-g hn19.fa\nsample.bam\nDetect translocations\n```\n### Detecting translocations\n```\ndelly\n-t TRA\n-x excludeList.tsv\n-o sample.jumpy.bam\n-q 0\n-g hn19.fa\nsample.bam\n```\n### Post-processing\nEach DELLY tool produces several files, which will all need to be merged together after the chromosomes are finished processing. The output format is described on the DELLY webpage. The merging script may require a small parser to combine the output from multiple runs in together.\nMerge DELLY results with vcftools\n\n## Overview\n\n## Dependencies\n\n* [picard 2.19.2](https://master.dl.sourceforge.net/project/picard/picard-tools/1.89/picard-tools-1.89.zip)\n* [java 8](https://github.com/AdoptOpenJDK/openjdk8-upstream-binaries/releases/download/jdk8u222-b10/OpenJDK8U-jdk_x64_linux_8u222b10.tar.gz)\n* [delly 0.9.1](https://github.com/dellytools/delly/releases/download/v0.9.1/delly_v0.9.1_linux_x86_64bit)\n* [bcftools 1.9](https://github.com/samtools/bcftools/releases/download/1.9/bcftools-1.9.tar.bz2)\n* [tabix 0.2.6](https://sourceforge.net/projects/samtools/files/tabix/tabix-0.2.6.tar.bz2)\n* [vcftools 0.1.16](https://github.com/vcftools/vcftools/archive/v0.1.16.tar.gz)\n\n\n## Usage\n\n### Cromwell\n```\njava -jar cromwell.jar run delly.wdl --inputs inputs.json\n```\n\n### Inputs\n\n#### Required workflow parameters:\nParameter|Value|Description\n---|---|---\n`inputTumor`|File|Tumor input .bam file.\n`outputFileNamePrefix`|String|Output prefix to be used with result files.\n`reference`|String|the reference genome for input sample\n\n\n#### Optional workflow parameters:\nParameter|Value|Default|Description\n---|---|---|---\n`inputNormal`|File?|None|Normal input .bam file.\n`markdup`|Boolean|true|A switch between marking duplicate reads and indexing with picard.\n\n\n#### Optional task parameters:\nParameter|Value|Default|Description\n---|---|---|---\n`dupmarkBam.jobMemory`|Int|20|memory allocated for Job\n`dupmarkBam.timeout`|Int|20|Timeout in hours\n`dupmarkBam.modules`|String|\"java/8 picard/2.19.2\"|Names and versions of modules for picard-tools and java\n`runDelly.mappingQuality`|Int|30|defines quality threshold for reads to use in calling SVs. Set higher for big data\n`runDelly.translocationQuality`|Int|20|min. PE quality for translocation\n`runDelly.insertSizeCutoff`|Int|9|insert size cutoff, median+s*MAD (deletions only). Set higher for big data\n`runDelly.minClip`|Int|25|min. clipping length\n`runDelly.minCliqueSize`|Int|2|min. PE/SR clique size. Set to 5 for big data\n`runDelly.minRefSeparation`|Int|25|min. reference separation\n`runDelly.maxReadSeparation`|Int|40|Maximum read separation\n`runDelly.additionalParameters`|String?|None|Any additional parameters to delly we want to pass\n`runDelly.jobMemory`|Int|16|memory allocated for Job\n`runDelly.timeout`|Int|20|Timeout in hours\n`mergeAndZipALL.modules`|String|\"bcftools/1.9 vcftools/0.1.16 tabix/0.2.6\"|Names and versions of modules for picard-tools and java\n`mergeAndZipALL.variantSupport`|Int|0|Paired-end support for structural variants, in pairs. Default is 10\n`mergeAndZipALL.jobMemory`|Int|10|memory allocated for Job\n`mergeAndZipFiltered.modules`|String|\"bcftools/1.9 vcftools/0.1.16 tabix/0.2.6\"|Names and versions of modules for picard-tools and java\n`mergeAndZipFiltered.variantSupport`|Int|0|Paired-end support for structural variants, in pairs. Default is 10\n`mergeAndZipFiltered.jobMemory`|Int|10|memory allocated for Job\n\n\n### Outputs\n\nOutput | Type | Description | Labels\n---|---|---|---\n`mergedIndex`|File|tabix index of the vcf file containing all structural variant calls|vidarr_label: mergedIndex\n`mergedVcf`|File|vcf file containing all structural variant calls|vidarr_label: mergedVcf\n`mergedFilteredIndex`|File?|tabix index of the filtered vcf file containing structural variant calls|vidarr_label: mergedFilteredIndex\n`mergedFilteredVcf`|File?|filtered vcf file containing structural variant calls|vidarr_label: mergedFilteredVcf\n`mergedFilteredPassIndex`|File?|tabix index of the filtered vcf file containing PASS structural variant calls|vidarr_label: mergedFilteredPassIndex\n`mergedFilteredPassVcf`|File?|filtered vcf file containing PASS structural variant calls|vidarr_label: mergedFilteredPassVcf\n\n\n## Commands\nThis section lists command(s) run by delly workflow\n \n* Running delly\n \nSV calling workflow\n \n### Mark duplicates\n \n```\n   This is a job which can be optional:  \n \n   java -Xmx[JOB_MEMORY-8]G -jar picard.jar MarkDuplicates \n                                 TMP_DIR=picardTmp\n                                 ASSUME_SORTED=true \n                                 VALIDATION_STRINGENCY=LENIENT \n                                 OUTPUT=INPUT_BAM_BASENAME_dupmarked.bam\n                                 INPUT=INPUT_BAM\n                                 CREATE_INDEX=true \n                                 METRICS_FILE=INPUT_BAM_BASENAME.mmm\n```\n \n### Call variants\n \n```\n delly call -t DELLY_MODE\n       -x EXCLUDE_LIST\n       -o SAMPLE_NAME.DELLY_MODE.CALL_TYPE.bcf\n       -q MAPPING_QUALITY\n       -s INSERT_SIZE_CUTOFF\n       -r ~{translocationQuality} \\\n       -c ~{minClip} \\\n       -z ~{minCliqueSize} \\\n       -m ~{minRefSeparation} \\\n       -n ~{maxReadSeparation} \\\n       -g REF_FASTA\n          ADDITIONAL_PARAMETERS\n          INPUT_BAM\n \n    Optional post-filtering if we need somatic variants:\n \n    echo \"Somatic mode requested, will run delly filtering for somatic SVs\"\n    bcftools view SAMPLE_NAME.DELLY_MODE.CALL_TYPE.bcf | grep ^# | tail -n 1 | \n             sed 's/.*FORMAT\\t//' | awk -F \"\\t\" '{print $1\"\\ttumor\";print $2\"\\tcontrol\"}' \u003e samples.tsv\n    delly filter -f somatic -o SAMPLE_NAME.DELLY_MODE.CALL_TYPE.bcf -s samples.tsv \n    bcftools view SAMPLE_NAME.DELLY_MODE.CALL_TYPE_filtered.bcf | \n    bgzip -c \u003e SAMPLE_NAME.DELLY_MODE.CALL_TYPE_filtered.vcf.gz\n \n \n bcftools view SAMPLE_NAME.DELLY_MODE.CALL_TYPE.bcf | bgzip -c \u003e SAMPLE_NAME.DELLY_MODE.CALL_TYPE.vcf.gz\n \n tabix -p vcf SAMPLE_NAME.DELLY_MODE.CALL_TYPE.vcf.gz\n tabix -p vcf SAMPLE_NAME.DELLY_MODE.CALL_TYPE_filtered.vcf.gz\n \n```\n \n### Post-process\n \n```\n   vcf-concat INPUT_VCFS | vcf-sort | bgzip -c \u003e SAMPLE_NAME.DELLY_MODE.CALL_TYPE_PREFIX.delly.merged.vcf.gz\n   tabix -p vcf SAMPLE_NAME.DELLY_MODE.CALL_TYPE_PREFIX.delly.merged.vcf.gz\n \n   bcftools view -i \"%FILTER='PASS' \u0026 INFO/PE\u003e~{variantSupport}\" SAMPLE_NAME.DELLY_MODE.CALL_TYPE_PREFIX.delly.merged.vcf.gz -Oz -o SAMPLE_NAME.DELLY_MODE.CALL_TYPE_PREFIX.delly.merged.pass.vcf.gz\n   tabix -p vcf SAMPLE_NAME.DELLY_MODE.CALL_TYPE_PREFIX.delly.merged.pass.vcf.gz\n \n```\n## Support\n\nFor support, please file an issue on the [Github project](https://github.com/oicr-gsi) or send an email to gsi@oicr.on.ca .\n\n_Generated with generate-markdown-readme (https://github.com/oicr-gsi/gsi-wdl-tools/)_\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Foicr-gsi%2Fdelly","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Foicr-gsi%2Fdelly","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Foicr-gsi%2Fdelly/lists"}