From 3c789431bfd7c958f91a2062d7ea359a04a408f5 Mon Sep 17 00:00:00 2001
From: Redmar van den Berg <RedmarvandenBerg@lumc.nl>
Date: Mon, 25 Nov 2019 15:27:04 +0100
Subject: [PATCH] Update min-depth to integer
In the VCF files generated by GATK, DP is an integer, while the GQ field
holds a float.
##FORMAT=<ID=DP,Number=1,Type=Integer
##FORMAT=<ID=GQ,Number=1,Type=Float
---
README.md | 2 +-
vtools/cli.py | 2 +-
2 files changed, 2 insertions(+), 2 deletions(-)
diff --git a/README.md b/README.md
index b613410..8ace1a9 100644
--- a/README.md
+++ b/README.md
@@ -161,7 +161,7 @@ Options:
-s, --stats PATH Path to output stats json file
-dc, --discordant PATH Path to output discordant VCF file
-mq, --min-qual FLOAT Minimum quality of variants to consider
- -md, --min-depth FLOAT Minimum depth 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 eac0b48..f0079b2 100644
--- a/vtools/cli.py
+++ b/vtools/cli.py
@@ -39,7 +39,7 @@ from .gcoverage import RefRecord, region_coverages
required=False)
@click.option("-mq", "--min-qual", type=float,
help="Minimum quality of variants to consider", default=30)
-@click.option("-md", "--min-depth", type=float,
+@click.option("-md", "--min-depth", type=int,
help="Minimum depth of variants to consider", default=0)
def evaluate_cli(call_vcf, positive_vcf, call_samples, positive_samples,
min_qual, min_depth, stats, discordant_vcf):
--
GitLab