update docs

docs/extras/vcf_annotator.md

@@ -20,10 +20,10 @@ The tool uses a SeqRepo data proxy. By default, the local instance at `/usr/loca
 Example of how to run:
 
 ```commandline
-python3 -m src.ga4gh.vrs.extras.vcf_annotation --vcf_in input.vcf.gz --vcf_out output.vcf.gz --vrs_pickle_out vrs_objects.pkl
+python3 -m src.ga4gh.vrs.extras.vcf_annotation input.vcf.gz --vcf_out output.vcf.gz --vrs_pickle_out vrs_objects.pkl
 ```
 
-`--vcf_in` specifies the path of the input VCF file to annotate. `--vcf_out` specifies the path of the output annotated VCF file. The `--vrs_pickle_out` specifies the path of the output pickle file containing VRS data (Both vcf_out and vrs_pickle_out are optional, but at least one __must__ be provided).
+Pass the path of the input VCF file as the argument to the script. Use either `--vcf_out` to specify the path of the output annotated VCF file, or `--vrs_pickle_out` to specify the path of the output pickle file containing VRS data (both `vcf_out` and `vrs_pickle_out` are optional, but at least one __must__ be provided).
 
 ### Use local SeqRepo Data Proxy with different
 
@@ -32,7 +32,7 @@ You can change the root directory of SeqRepo by using `seqrepo_root_dir`.
 To use the local SeqRepo data proxy with SeqRepo root directory at `vrs-python/seqrepo/latest`:
 
 ```commandline
-python3 -m src.ga4gh.vrs.extras.vcf_annotation --vcf_in input.vcf.gz --vcf_out output.vcf.gz --vrs_pickle_out vrs_objects.pkl --seqrepo_root_dir vrs-python/seqrepo/latest
+python3 -m src.ga4gh.vrs.extras.vcf_annotation input.vcf.gz --vcf_out output.vcf.gz --vrs_pickle_out vrs_objects.pkl --seqrepo_root_dir vrs-python/seqrepo/latest
 ```
 
 ### Use the REST SeqRepo Data Proxy with default base url
@@ -42,15 +42,15 @@ You can change the data proxy type by using: `--seqrepo_dp_type` (options are `l
 To use the REST SeqRepo data proxy at default url: `http://localhost:5000/seqrepo`:
 
 ```commandline
-python3 -m src.ga4gh.vrs.extras.vcf_annotation --vcf_in input.vcf.gz --vcf_out output.vcf.gz --vrs_pickle_out vrs_objects.pkl --seqrepo_dp_type rest
+python3 -m src.ga4gh.vrs.extras.vcf_annotation input.vcf.gz --vcf_out output.vcf.gz --vrs_pickle_out vrs_objects.pkl --seqrepo_dp_type rest
 ```
 
 ### Use the REST SeqRepo Data Proxy with different base url
 You can change the SeqRepo REST base url by using: `--seqrepo_base_url`.
 
 To use the REST SeqRepo data proxy, at custom url: `http://custom.url:5000/seqrepo`:
 ```commandline
-python3 -m src.ga4gh.vrs.extras.vcf_annotation --vcf_in input.vcf.gz --vcf_out output.vcf.gz --vrs_pickle_out vrs_objects.pkl --seqrepo_dp_type rest --seqrepo_base_url http://custom.url:5000/seqrepo
+python3 -m src.ga4gh.vrs.extras.vcf_annotation input.vcf.gz --vcf_out output.vcf.gz --vrs_pickle_out vrs_objects.pkl --seqrepo_dp_type rest --seqrepo_base_url http://custom.url:5000/seqrepo
 ```
 
 ### Other Options
@@ -67,4 +67,4 @@ python3 -m src.ga4gh.vrs.extras.vcf_annotation --vcf_in input.vcf.gz --vcf_out o
 >Require validation checks to pass in order to return a VRS object
 
 `--help`
->Show the options available
+>Show the options available