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Update README.md
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Co-authored-by: Dan Miller <dmiller15@users.noreply.github.com>
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migbro and dmiller15 committed Sep 17, 2024
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Expand Up @@ -54,7 +54,7 @@ Note: Not all outputs are available from the Kids First Portal. If there is an o
- `collectvariantcallingmetrics`: Variant calling summary and detailed metrics files
- `peddy_html`: html summary of peddy results
- `peddy_ped`: ped format summary of peddy results
- `cgp_vep_annotated_vcf`: Variant Effect Predictor annotated VCF files. File suffix tyically `.multi.vqsr.filtered.denovo.vep_105.vcf.gz` .Contains joint calls with the following:
- `cgp_vep_annotated_vcf`: Variant Effect Predictor annotated VCF files. File suffix tyically `.multi.vqsr.filtered.denovo.vep_105.vcf.gz`. Contains joint calls with the following:
- `lowGQ` FILTER `GQ < 20.0`.
- Genotype posterior probabilities. See [here](https://gatk.broadinstitute.org/hc/en-us/articles/360037226592-CalculateGenotypePosteriors) for an explanation
- INFO tags of `hiConfDeNovo`, `loConfDeNovo`. See [here](https://gatk.broadinstitute.org/hc/en-us/articles/4409924802331-PossibleDeNovo) for more info
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