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Update README.md
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mirgin01 authored Sep 5, 2024
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Expand Up @@ -38,7 +38,6 @@ csv_folder='csv/examples/'
output_docs_folder='output_docs/CINECA_dataset/'

#### VCF Conversion config parameters ####
num_variants=100000
reference_genome='GRCh37' # Choose one between NCBI36, GRCh37, GRCh38
```

Expand All @@ -62,7 +61,7 @@ First option will delete "_id" entries generated by mongoDB:
```bash
docker exec ri-tools-mongo mongoexport --jsonArray --uri "mongodb://root:[email protected]:27017/beacon?authSource=admin" --collection genomicVariations | sed '/"_id":/s/"_id":[^,]*,//g' > genomicVariations.json
```
The second one will keep the "_id" entries generated by mongoDB:
The second option, our **recommended one**, will keep the "_id" entries generated by mongoDB:
```bash
docker exec ri-tools-mongo mongoexport --jsonArray --uri "mongodb://root:[email protected]:27017/beacon?authSource=admin" --collection genomicVariations > genomicVariations.json
```
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