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Update CombineBatches workflow #732

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Update CombineBatches workflow #732

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Commits on Oct 3, 2024

  1. Add cluster_batch_format.py; clean up MCNV formatting 

    Add reformatting to GenotypeBatch

Expose reformat_script

Start ripping stuff out

Finish rewriting wdl and template

Add TODO and delete unused task
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    mwalker174 committed Oct 3, 2024
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  2. Don't assign genotypes to CNVs in add_genotypes.py

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  3. Set mixed_breakend_window to 1mb

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  4. Fixes

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  5. Start implementing ContextAwareClustering

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  6. Fix wdl

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  7. Update wdl and gatk docker

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  8. Comment

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  9. Set context overlap parameters

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  10. Update docker

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  11. Fix size in ReformatGenotypedVcf

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  12. Update to reformat_genotyped_vcf.py

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  13. Update legacy reformatter, fix GenotypeBatchMetrics wdl

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  14. Remove reformat step from GenotypeBatch

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  15. Use RD_CN if CN is unavailable for mCNVs in svtk vcf2bed

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  16. Add additional_args to svcluster and groupedsvcluster

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  17. Add join step

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  18. Update runtime attr

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  19. Filter legacy records with invalid coords (needs testing)

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  20. Fix record dropping; add --fix-end to wdl call

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  21. Representative breakpoint summary strategy

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  22. Update gatk docker

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  23. Integerate SR flags into VCF

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  24. Update dockers

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  25. Parse last column in SR flags lists

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  26. Gatk to svtk formatting

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  27. Fix CNV strands and overlap breakpoint filter bothside pass file parsing

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  28. Breakpoint overlap filter now sorts by BOTHSIDES_SUPPORT status rathe… 

    …r than fraction
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  29. Set empty FILTER statuses to PASS

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  30. Use safer get() methods instead of brackets for accessing FORMAT fields

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  31. Update dockers

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  32. Delete unused VcfClusterSingleChromsome.wdl

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  33. Remove other unused wdls

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  34. Do not require CN or RD_CN to be defined for all samples for CNVs in … 

    …get_called_samples()
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    mwalker174 committed Oct 3, 2024
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Commits on Oct 4, 2024

  1. Fix multi-allelic ALTs and genotype parsing

    @mwalker174
    mwalker174 committed Oct 4, 2024
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  2. Update dockers

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    mwalker174 committed Oct 4, 2024
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