Update README to link to SV callers used. #541

kirtanav98 · 2023-05-25T17:17:46Z

Description
I Updated the README to link to each of the raw callers used by GATK-SV: Manta, Wham, cn.MOPS, and GATK-gCNV using links from the SV information article.
I also added a link to the GATK tool SVAnnotate under AnnotateVcf > functional annotation.

Changes Made
Added links to the SV callers where appropriate.

Related Issue
Successfully merging this pull request will resolve issue #537.

epiercehoffman

Thanks for working on this, Kirtana! This will be a really great improvement to our documentation so that users can easily find more information on the tools we use.

I've requested some changes to make sure these documentation changes are as clear as possible - let me know if you have any questions or alternative suggestions.

I don't think it makes sense to add the raw callers other than MELT under "Deployment and execution" because (excluding MELT) they are integrated directly into the GATK-SV pipeline, so there is no additional requirement for users to install that software outside of GATK-SV. Instead, let's add the links to existing parts of the documentation where the tools are already named. And I think we can stick with just links since the README is mostly technical documentation - so no need to describe the tools in detail.

I think there are multiple places where adding these links could make sense - ie. under "Pipeline Overview" or "Module Descriptions." I think I would personally go with adding the raw caller links under "Module Descriptions" because those are the sections that contain more detail about applying each of the tools (but you could also choose to add them under "Pipeline Overview" because that is where they are first mentioned). So that would be the GatherSampleEvidence section for MELT, Manta, and Wham, and the GatherBatchEvidence section for cn.MOPS and GATK-gCNV. I would probably additionally add an extra link to gCNV under "gCNV training" because that section contains more detail on gCNV.

README.md

Update with fixes to location of annotations Co-authored-by: epiercehoffman <epierceh@broadinstitute.org>

Fixed location of links based on review

kirtanav98 · 2023-05-30T14:49:54Z

Thank you for your feedback. The changes have been addressed here and here.

epiercehoffman

Thank you for making those changes so quickly! It's looking really good, just requesting a couple of small tweaks this time

epiercehoffman · 2023-05-30T22:58:26Z

README.md

@@ -250,7 +250,7 @@ Note: a list of sample IDs must be provided. Refer to the [sample ID requirement
 * Per-sample BAM or CRAM files aligned to hg38. Index files (`.bai`) must be provided if using BAMs.

 #### Outputs:
-* Caller VCFs (Manta, MELT, and/or Wham)
+* Caller VCFs ([Manta](https://github.com/Illumina/manta), [MELT](https://melt.igs.umaryland.edu/), and/or [Wham](https://github.com/zeeev/wham))


Can we move these links up to the GatherSampleEvidence summary on line 245 to match the way you did it for GatherBatchEvidence?

Yes. They are linked there and addressed here.

README.md

epiercehoffman · 2023-05-30T23:05:43Z

README.md

@@ -287,7 +287,7 @@ The purpose of sample filtering at this stage after EvidenceQC is to prevent ver


 ## <a name="gcnv-training">TrainGCNV</a>
-Trains a gCNV model for use in [GatherBatchEvidence](#gather-batch-evidence). The WDL can be found at `/wdl/TrainGCNV.wdl`. See the [gCNV training overview](#gcnv-training-overview) for more information.
+Trains a [gCNV](https://gatk.broadinstitute.org/hc/en-us/articles/360035531152) model for use in [GatherBatchEvidence](#gather-batch-evidence). The WDL can be found at `/wdl/TrainGCNV.wdl`. See the [gCNV training overview](#gcnv-training-overview) for more information.


Can you also link to gCNV under "gCNV training" (line 200) since that appears earlier in the README? Sorry if this was confusing in my last comment since there are two sections on gCNV training. It's fine to either leave this link or remove it once you add the other one, since the two sections link to each other

Yes. That link is added and addressed here.

Added links to line 245

Co-authored-by: epiercehoffman <epierceh@broadinstitute.org>

Added extra link to gCNV in description of train gCNV

Added back in the previous link in line 200 and removed the additional links under gCNV

README.md

Co-authored-by: epiercehoffman <epierceh@broadinstitute.org>

epiercehoffman

Looks good! Thanks for working on this and for your patience with ironing out all the little details! You can go ahead and merge this.

* Update README to link to SV callers used. * Update README.md Update with fixes to location of annotations Co-authored-by: epiercehoffman <epierceh@broadinstitute.org> * Update README.md Fixed location of links based on review * Update README.md Added links to line 245 * Update README.md Co-authored-by: epiercehoffman <epierceh@broadinstitute.org> * Update README.md Added extra link to gCNV in description of train gCNV * Update README.md Added back in the previous link in line 200 and removed the additional links under gCNV * Update README.md Co-authored-by: epiercehoffman <epierceh@broadinstitute.org> * Update README.md Co-authored-by: epiercehoffman <epierceh@broadinstitute.org> * Update README.md Co-authored-by: epiercehoffman <epierceh@broadinstitute.org> --------- Co-authored-by: Kirtana Veeraraghavan <kveerara@wmbee-8ec.broadinstitute.org> Co-authored-by: epiercehoffman <epierceh@broadinstitute.org>

* Revert to CPG commit ca70123 * Absorb Broad upstream changes: * Add handling for Flag vcf fields to vcf_to_pandas (broadinstitute#506) * add outlier samples list & count outputs to PlotSVCountsPerSample (broadinstitute#510) * eliminate cram to bam conversion when possible (broadinstitute#468) * Add ref panel inputs for MakeCohortVcf subworkflows (broadinstitute#517) * Extend STR workflow to collect additional locus-level metrics (broadinstitute#516) * Change ref allele to N if unsupported in gatk formatting script (broadinstitute#511) * Add sample renaming for SD files in GatherBatchEvidence (broadinstitute#519) * Remove vcf header contig sorting in CleanVcf5 (broadinstitute#518) * Add support for building dockers for multiple registries. (broadinstitute#507) * Remove non-public images from the git-sha-based target determination (broadinstitute#525) * Fix ReadMe for build docker (broadinstitute#528) * Fix for tiny shard of IntegrateGQ in single sample pipeline (broadinstitute#524) * Fix issue in Genotype batch script with low PE_log_pval causing zero PE_count (broadinstitute#527) * Manually install MASS R package in sv-pipeline-virtual-env (broadinstitute#534) * Fix non-deterministic errors in GetSampleIdsFromVcfTar (broadinstitute#531) * Add ApplyManualVariantFilter json template (broadinstitute#536) * make the RunMELT task a little more robust (broadinstitute#529) * Improve STR workflow (broadinstitute#539) * Fix workspace format (Generate Terra workspace tsv files from transposed tables) (broadinstitute#523) * Update VaPoR workflows (broadinstitute#532) * Update README to link to SV callers used. (broadinstitute#541) Co-authored-by: Mark Walker <markw@broadinstitute.org> Co-authored-by: epiercehoffman <epierceh@broadinstitute.org>

Update README to link to SV callers used.

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kirtanav98 requested a review from epiercehoffman May 25, 2023 17:18

epiercehoffman requested changes May 25, 2023

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kirtanav98 and others added 2 commits May 30, 2023 09:58

Update README.md

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Update with fixes to location of annotations Co-authored-by: epiercehoffman <epierceh@broadinstitute.org>

Update README.md

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Fixed location of links based on review

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kirtanav98 and others added 4 commits May 31, 2023 09:10

Update README.md

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Added links to line 245

Update README.md

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Co-authored-by: epiercehoffman <epierceh@broadinstitute.org>

Update README.md

7b9363d

Added extra link to gCNV in description of train gCNV

Update README.md

198a2a4

Added back in the previous link in line 200 and removed the additional links under gCNV

epiercehoffman reviewed Jun 2, 2023

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kirtanav98 and others added 3 commits June 2, 2023 14:06

Update README.md

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Co-authored-by: epiercehoffman <epierceh@broadinstitute.org>

Update README.md

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Co-authored-by: epiercehoffman <epierceh@broadinstitute.org>

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kirtanav98 requested a review from epiercehoffman June 2, 2023 18:07

epiercehoffman approved these changes Jun 2, 2023

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kirtanav98 merged commit bd85b0a into main Jun 2, 2023

kirtanav98 deleted the kv_modify_readme_with_links branch June 2, 2023 18:17

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Update README to link to SV callers used. #541

Update README to link to SV callers used. #541

kirtanav98 commented May 25, 2023

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Update README to link to SV callers used. #541

Update README to link to SV callers used. #541

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