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Update v4 HTs help page for v4.1.1#1836

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ch-kr wants to merge 14 commits intomainfrom
kc/update_hts_help
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Update v4 HTs help page for v4.1.1#1836
ch-kr wants to merge 14 commits intomainfrom
kc/update_hts_help

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@ch-kr ch-kr commented Jan 21, 2026

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@ch-kr ch-kr marked this pull request as draft January 21, 2026 17:15
@ch-kr ch-kr self-assigned this Jan 21, 2026
@ch-kr ch-kr marked this pull request as ready for review January 28, 2026 16:22
@ch-kr ch-kr requested a review from klaricch January 28, 2026 16:22
- `vep_versions`: Ensembl VEP version (115).
- `vep_help`: Output from `vep --help`.
- `vep_config`: Ensembl VEP configuration to run VEP 115 version with [Hail](https://hail.is/docs/0.2/methods/genetics.html#hail.methods.vep). File created using command within VEP init shell script in https://github.com/broadinstitute/gnomad_methods/tree/main.
- `gencode_version`: Dictionary of GENCODE version used in Ensembl VEP 115.
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why a dictionary here?

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oops, this is when I thought we'd merge the 105 and 115 globals. will revert

ch-kr and others added 3 commits January 30, 2026 11:01
@ch-kr ch-kr requested a review from klaricch January 30, 2026 16:07
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lgtm!

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