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Remove mention of variant filtering from GenerateBatchMetrics documentation #769

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merged 3 commits into from
Jan 9, 2025
Merged

Remove mention of variant filtering from GenerateBatchMetrics documentation #769

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kjaisingh Jan 8, 2025
fe1672c
Remove filtering from GenerateBatchMetrics docs
kjaisingh Jan 9, 2025
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Merge branch 'main' into kj_minor_docs_fix
kjaisingh Jan 9, 2025
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2 changes: 1 addition & 1 deletion website/docs/execution/joint.md
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Expand Up @@ -66,7 +66,7 @@ algorithms (Manta, MELT, and Wham), read depth (RD), split read positions (SR),
6. `04-GatherBatchEvidence`: Per-batch copy number variant calling using cn.MOPS and GATK gCNV; B-allele frequency (BAF)
generation; call and evidence aggregation
7. `05-ClusterBatch`: Per-batch variant clustering
8. `06-GenerateBatchMetrics`: Per-batch variant filtering, metric generation
8. `06-GenerateBatchMetrics`: Per-batch metric generation
9. `07-FilterBatchSites`: Per-batch variant filtering and plot SV counts per sample per SV type to enable choice of IQR
cutoff for outlier filtration in `08-FilterBatchSamples`
10. `08-FilterBatchSamples`: Per-batch outlier sample filtration
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