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Pull requests list

Create SampleQC and Batching notebooks enhancement New feature or request
#744 opened Nov 5, 2024 by kjaisingh Loading…
@kjaisingh
Remove internal workflows and scripts
#742 opened Oct 31, 2024 by mwalker174 Loading…
Migrate CleanVcf into GATK
#733 opened Oct 17, 2024 by kjaisingh • Draft
@kjaisingh
Update CombineBatches workflow
#732 opened Oct 3, 2024 by mwalker174 • Draft
Keep unresolved Manta calls
#723 opened Sep 11, 2024 by CuriousTim Loading…
4
Filter outlier samples in TrainGCNV and GenerateBatchMetrics enhancement New feature or request
#717 opened Aug 26, 2024 by kjaisingh Loading…
1
@kjaisingh
use chrX and chrY to match sex chromosomes
#713 opened Aug 19, 2024 by CuriousTim Loading…
7
Add documentation for the de-novo pipeline
#675 opened May 13, 2024 by VJalili • Draft
2 tasks
12
Refactor workflow inputs/output for consistency
#668 opened Apr 25, 2024 by VJalili • Draft
2 tasks done
Scripts to create downsampled files
#662 opened Apr 2, 2024 by VJalili Loading…
4 tasks done
Remove outliers across per-contig VCFs
#654 opened Mar 11, 2024 by epiercehoffman • Draft
Workflow to apply NCR and reference artifact filters and remove zero-carrier sites
#653 opened Mar 8, 2024 by epiercehoffman • Draft
1
fix: add sd_locs_vcf_index input to SDtoBAF
#644 opened Feb 12, 2024 by simojoe Loading…
1
2
Change default behavior of GatherSampleEvidence to skip running module metrics
#633 opened Jan 31, 2024 by VJalili • Draft
4
Removed pairwise batch effect checks from WDL workflow
#617 opened Nov 9, 2023 by shadizaheri Loading…
4
Add TransferVcfAnnotations workflow
#533 opened May 11, 2023 by mwalker174 • Draft
Extend functionality for outlier sample exclusion workflow
#496 opened Feb 11, 2023 by RCollins13 Loading…
4
Add reclustering WDLs (do not merge)
#446 opened Oct 12, 2022 by mwalker174 • Draft
Update batch effect workflows
#435 opened Oct 5, 2022 by mwalker174 Loading…
an alpha version of a report generator that creats a report of the re…
#416 opened Sep 23, 2022 by shadizaheri Loading…
@VJalili
1
KN Picard Metrics Aggregation Script
#364 opened Jun 29, 2022 by krithikanathamuni • Draft
21
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