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LOG.md

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Version Updates

v1.1.0

  • Conversion to YAML format for portal objects

v1.0.0

  • v3 -> v1.0.0, we are starting a new more comprehensive versioning system
  • Added some change in metaworkflows to accomodate the changes in foursight
  • Updated docker images

v3

  • Changes in repo structure to allow for compatibility with new pipeline organization
  • Pipeline renamed from cnv to sv_germline
  • Step 8 (Cytoband annotation) renamed to secondary annotation. Additional annotations added on top of the existing Cytoband annotation. Worst consequence and breakpoint location(s) relative to transcripts are now reported as well as liftover of each breakpoint (if present in hg19). Filtering of transcript by Biotype implemented here as well, with variants being dropped if they no longer have any transcripts after this filter
  • Updated SV_annotation_VCF_cleaner script to remove Cytoband and liftover annotations from the vcf file to be visualized by HiGlass for faster loading

v2

  • The pipeline has been converted to work on private ECR images which are created from our public Docker images
  • Various updates throughout the CGAP SV Pipeline. The current pipeline is outlined below and updates are indicated. A new version of granite (v0.1.13) is being used for steps 2-13 of the pipeline.
    • Step 1. Manta-based calling of SVs (Update: manta now uses the callRegions flag instead of regions. We no longer use get_contigs.py from Parliament2 and have removed the Parliament2 github repo from the cgap-manta:v2 Dockerfile)
    • Step 2. Granite SVqcVCF is used to count DEL and DUP variants and provide a total number of DEL and DUP variants in each sample (New Step)
    • Step 3. VEP/sansa annotation (Update: VEP now includes the canonical flag to identify the canonical transcript for each gene)
    • Step 4. Granite SVqcVCF is used to count DEL and DUP variants and provide a total number of DEL and DUP variants in each sample (New Step)
    • Step 5. Annotation filtering and SV type selection
    • Step 6. 20 Unrelated filtering (Update: New 20 unrelated reference file resulting from UGRP samples re-mapped with v24 of the CGAP Pipeline including alt index)
    • Step 7. Granite SVqcVCF is used to count DEL and DUP variants and provide a total number of DEL and DUP variants in each sample (New Step)
    • Step 8. Cytoband annotation step adds the Cytoband for each breakpoint; Cyto1 and Cyto2 (New Step)
    • Step 9. Granite SVqcVCF is used to count DEL and DUP variants and provide a total number of DEL and DUP variants in each sample (New Step)
    • Step 10. Length filtering
    • Step 11. Granite SVqcVCF is used to count DEL and DUP variants and provide a total number of DEL and DUP variants in each sample (New Step)
    • Step 12. Annotation cleaning to produce a vcf file that loads quickly in the Higlass genome browser
    • Step 13. Granite SVqcVCF is used to count DEL and DUP variants and provide a total number of DEL and DUP variants in each sample (New Step)

v1

  • Created entirely new pipeline - CGAP Structural Variant (SV) Pipeline
    • Step 1. Manta-based SV calling to generate a vcf file containing SVs in proband or trio
    • Step 2. VEP annotation for genes/transcripts and sansa annotation for gnomAD SV population allele frequencies
    • Step 3. Annotation filter to remove non-coding SVs, SVs with high allele frequency in gnomAD SV, and select for only deletions (SVTYPE=DEL) and duplications (SVTYPE=DUP)
    • Step 4. 20 Unrelated filtering to remove common and artefactual SVs compared to 20 unrelated samples that were also run through manta
    • Step 5. Length-based filtering to remove very long variants that are likely false positives and create issues when ingested into CGAP Portal due to the size of the associated gene list
    • Step 6. Annotation cleaning to produce a vcf file that loads quickly in the Higlass genome browser