From e63091633774a3690f7a7929e37d87f553e4e3a1 Mon Sep 17 00:00:00 2001
From: Redmar van den Berg <RedmarvandenBerg@lumc.nl>
Date: Mon, 25 Nov 2019 15:55:11 +0100
Subject: [PATCH] The discordant VCF file is gzipped
---
README.md | 2 +-
vtools/cli.py | 2 +-
2 files changed, 2 insertions(+), 2 deletions(-)
diff --git a/README.md b/README.md
index 8ace1a9..0d707d8 100644
--- a/README.md
+++ b/README.md
@@ -159,7 +159,7 @@ Options:
-ps, --positive-samples TEXT Sample(s) in positive-vcf to consider. May be
called multiple times [required]
-s, --stats PATH Path to output stats json file
- -dc, --discordant PATH Path to output discordant VCF file
+ -dc, --discordant PATH Path to output gzipped discordant vcf file
-mq, --min-qual FLOAT Minimum quality of variants to consider
-md, --min-depth INTEGER Minimum depth of variants to consider
--help Show this message and exit.
diff --git a/vtools/cli.py b/vtools/cli.py
index 37ea32f..97ee6df 100644
--- a/vtools/cli.py
+++ b/vtools/cli.py
@@ -35,7 +35,7 @@ from .gcoverage import RefRecord, region_coverages
@click.option("-s", "--stats", type=click.Path(writable=True),
help="Path to output stats json file")
@click.option("-dvcf", "--discordant-vcf", type=click.Path(writable=True),
- help="Path to output discordant VCF file",
+ help="Path to output gzipped discordant vcf file",
required=False)
@click.option("-mq", "--min-qual", type=float,
help="Minimum quality of variants to consider", default=30)
--
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