20765: Adding gvcf regions subdir.

[lightning.git] / gvcf_regions / README.md

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+[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].
+```