📚 update docs for genotype filtering #57
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dmiller15
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migbro
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docs/GATK_GERMLINE_README.md
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| small-scale experiments, such as targeted gene panels or exome studies with | ||
| fewer than 30 exomes." Therefore, VQSR is only activated in this workflow when | ||
| the input gVCFs for this workflow come from whole genome sequencing experiments | ||
| or when the user provides 30 or more exome gVCFs. |
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If you provide 30+ exomes, target, do you get a joint called VCF, or individual calls with VQSR?
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They all get jointly processed. 30+ exomes will go to VQSR, 30+ targeted will still be hard filtered.
Targeted seq just is too high depth and too low data to work properly in VQSR.
| Hard Filtering is really only constrained by having sufficient depth. In the | ||
| case of exome and targeted sequencing, the depths are more than sufficient. Our | ||
| current approach for hard filtering mirrors the default approach outlined in | ||
| the GATK documentation. However as they point out, "You absolutely SHOULD |
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Is there link to the various filtering possibilities/syntax?
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There are but they are GATK doc links, which means they'll just end up dead sooner or later.
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I'm debating making archive links to everything, but in the ticket.
wongjessica93
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* 🚧 restrucutre genotyping wf * 🚧 rework fitlering and defaults * 🚧 rework hardfiltering 🐛 fix typos 🧹 cleanup unused tools 🧹 return old output name * 🔧 update snv ports for genotyping * update docker table (#56) Co-authored-by: dmiller15 <[email protected]> * 📚 update docs for genotype filtering (#57) * 📚 update docs for genotype filtering * 📚 clarify docs --------- Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
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Description
Updating the docs and pub app formatting for the genotyping workflow.
Part of https://d3b.atlassian.net/browse/BIXU-3800
Type of change
How Has This Been Tested?
Please describe the tests that you ran to verify your changes. Provide instructions so we can reproduce. Please also list any relevant details for your test configuration
Test Configuration:
Checklist: