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address review comments
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apriltuesday committed Oct 9, 2024
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Expand Up @@ -80,7 +80,9 @@ This is passed using the option `--metadata_json`.
These can be provided either in the metadata file directly, or on the command line using the `--vcf_files` and `--reference_fata` options.
Note that if you are using more than one reference FASTA, you **cannot** use the command line options; you must specify which VCF files use which FASTA files in the metadata.

VCF files can be either uncompressed or compressed (bgzipped). FASTA files must be uncompressed.
VCF files can be either uncompressed or compressed using bgzip.
Other types of compression are not allowed and will result in errors during validation.
FASTA files must be uncompressed.

## Execution

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