Update browser for gnomAD v4.1 (checklist)

[ch-kr]

Ticket to track various v4.1 data loading / update requests

Loading requests:

• Update parsing of SV and CNV files #1439 | (@phildarnowsky-broad) Update code parsing SV and CNV files to accommodate updates, including updated metrics order, updated genetic ancestry terms, update from using gender to sex karyotype and reload SV, CNVs
• (@rileyhgrant) Load demo with PCSK9 (see thread) to get feedback on new flags below
• (@rileyhgrant) Load demo that contains only new gene constraint results (HT path shared here; gs://gnomad/v4.1/constraint/metrics/gnomad.v4.1.constraint_metrics.ht)
• Load 4.1 short variant data into production #1463 | (@rileyhgrant, @nadeaujoshua) Reload short variant exome and genome data
• Update downloads page to include new v4.1 files #1443 | (@rileyhgrant) Update downloads page links to point to new data
• (riley to merge PRs, work done by methods team -- thank you!) Apply changes to help pages; current PRs:
  • Update gnomAD Hail Tables Help page #1430 | HT help page -- Qin added a few minor edits due to the slightly tweaked joint freq HT schema
  • Help page updates for v4.1 #1433 | v4.0>v4.1 updates -- this PR has been approved and is ready to go (note that I added a minor update to the dataset selection page on Apr 4)
  • Add exome capture help page #1456 | Exome capture regions
  • Add help topic for combined frequency statistics #1465 | describe new joint freq stats
  • Add new variant flag descriptions to help text #1476 | Add new flags to flags help page (new PR)
  • Update description for non-UKB exome subset #1488 | Update name of v4 non-UKB subset in dataset selection help page
  • Change combined frequency stats help page to describe union p-value #1492 | Update joint frequency stats page to reflect different tests used -- PR approved/ready
  • Allele count help page #1494 | Allele count help page -- PR approved/ready
• Expose the non_ukb v4 short variant subset #1448 (@phildarnowsky-broad)| Make non-ukbb a selectable subset

Updates:

• Add new flag to variants page when variant is not called in one data type #1423 | (@rileyhgrant) Add new flag indicating when a variant was not called in any data type
• Add new flag for variants with discrepant frequencies #1442 | (@rileyhgrant) Add new flag for variants with discrepant frequencies between the exomes and genomes
• Add number of samples in v4.0 subsets to stats page #1440 | (@rileyhgrant) Update stats page to include number of samples in the two of the v4.0 exomes subsets
• Update typos on stats page #1458 | (@rileyhgrant) Not necessarily v4.1, but update typos on stats page
• Create Post “2024-04-gnomad-v4-1” gnomad-blog#153 | -- Blog post is approved/ready

Feedback

• v4.1 demo requests #1475 | (@rileyhgrant) ticket tracking feedback on v4.1 demo browser

Will add updates if I've missed anything and as we create links for some of the topics above!

Also including v4.1 release checklist

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Moved to own issue for post v4 launch

• Stats page average SNVs per person (Add average SNVs per person to stats page #1507)

[rileyhgrant]

Closing as completed, will open tickets for cleanup as needed.