--- /dev/null
+[comment]: # Copyright (C) The Lightning Authors. All rights reserved.
+[comment]: # ()
+[comment]: # SPDX-License-Identifier: AGPL-3.0
+gVCF Regions
+========
+
+gVCF Regions is a command line tool that output the called regions of a gVCF file in BED format.
+It handles four main types of gVCFs (Complete Genomics, Freebayes, GATK), with the capability
+to customize the settings of 'called regions'.
+
+### gVCF Regions Command
+```
+gvcf_regions.py [-h] [--unreported_is_called]
+ [--ignore_phrases IGNORE_PHRASES [IGNORE_PHRASES ...]]
+ [--min_GQ MIN_GQ] [--min_QUAL MIN_QUAL]
+ [--pass_phrases PASS_PHRASES [PASS_PHRASES ...]]
+ [--gvcf_type {complete_genomics,freebayes,gatk}]
+ GVCF
+
+Output the called regions of a gvcf file to stdout in bed format.
+
+positional arguments:
+ GVCF input gvcf file, accept gzipped and unzipped files, or
+ "-" for stream
+
+optional arguments:
+ -h, --help show this help message and exit
+ --unreported_is_called
+ use this flag to treat unreported sites as called
+ --ignore_phrases IGNORE_PHRASES [IGNORE_PHRASES ...]
+ list of phrases considered as discarded, e.g., CNV,
+ ME. A line that contains any of the ignore phrases is
+ discarded.
+ --min_GQ MIN_GQ minimum GQ (Genotype Quality) considered as called
+ --min_QUAL MIN_QUAL minimum QUAL considered as called
+ --pass_phrases PASS_PHRASES [PASS_PHRASES ...]
+ list of phrases considered as called, e.g., PASS,
+ REFCALL. A line must contain any of the pass phrases
+ to be considered as called.
+ --gvcf_type {complete_genomics,freebayes,gatk}
+ type of gvcf output. [unreported_is_called,
+ ignore_phrases, min_GQ, min_QUAL, pass_phrases]
+ presets: complete_genomics: [True, ['CNV', 'INS:ME'],
+ None, None, ['PASS']]. freebayes: [False, None, None,
+ None, ['PASS']]. gatk: [False, None, 5, None, None].
+```