diff --git a/README.md b/README.md index b613410b6ffe284cb28941c0082fe203db03dd73..8ace1a9fa7bd2810a0a0ef1967e43fe66a234cf6 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 eac0b48a4dcf81ad66d3cb3b91731353faac7b40..f0079b2b6541669687a96c9c74e8f7587ed12796 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):