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rsasch committed May 8, 2024
1 parent 869c024 commit c40fd6f
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Showing 4 changed files with 6 additions and 6 deletions.
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Expand Up @@ -39,7 +39,7 @@ Note that, by default, the Exomes Beta workflow uses the Blended Genomes Interva

### What does it return as output?

The following files are stored in the Google Cloud Storage path specified in the `extract_output_gcs_dir` input.
The following files are stored in the Google Cloud Storage path specified in the `extract_output_gcs_dir` workflow input.

- Sharded joint VCF files, index files, the interval lists for each sharded VCF, and a list of the sample names included in the callset.
- Size of output VCF files in megabytes
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6 changes: 3 additions & 3 deletions scripts/variantstore/beta_docs/gvs-quickstart.md
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Expand Up @@ -16,16 +16,16 @@ To learn more about the GVS workflow, see the [Genomic Variant Store workflow ov

### What data does it require as input?

- Reblocked single sample GVCF files (`input_vcfs`)
- GVCF index files (`input_vcf_indexes`)
- Reblocked single sample GVCF files
- GVCF index files

Example GVCF and index files in the Data tab of the [GVS beta workspace](https://app.terra.bio/#workspaces/gvs-prod/Genomic_Variant_Store_Beta) are hosted in a public Google bucket and links are provided in the sample data table.

While the GVS has been tested with 250,000 single sample whole genome GVCF files as input, only datasets of up to 25,000 whole genomes are being used for beta testing.

### What does it return as output?

The following files are stored in the Google Cloud Storage path specified in the `extract_output_gcs_dir` input.
The following files are stored in the Google Cloud Storage path specified in the `extract_output_gcs_dir` workflow input.

- Sharded joint VCF files, index files, the interval lists for each sharded VCF, and a list of the sample names included in the callset.
- Size of output VCF files in MB
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Expand Up @@ -37,7 +37,7 @@ While the GVS has been tested with 250,000 single sample whole genome GVCF files

### What does it return as output?

The following files are stored in the Google Cloud Storage path specified in the `extract_output_gcs_dir` input.
The following files are stored in the Google Cloud Storage path specified in the `extract_output_gcs_dir` workflow input.

- Sharded joint VCF files, index files, the interval lists for each sharded VCF, and a list of the sample names included in the callset.
- Size of output VCF files in megabytes
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2 changes: 1 addition & 1 deletion scripts/variantstore/beta_docs/run-your-own-samples.md
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Expand Up @@ -42,7 +42,7 @@ Input GVCF files for the GVS workflow must include the annotations described in

### What does it return as output?

The following files are stored in the Google Cloud Storage path specified in the `extract_output_gcs_dir` input.
The following files are stored in the Google Cloud Storage path specified in the `extract_output_gcs_dir` workflow input.

- Sharded joint VCF files, index files, the interval lists for each sharded VCF, and a list of the sample names included in the callset.
- Size of output VCF files in MB
Expand Down

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