diff --git a/README.md b/README.md index 8ace1a9fa7bd2810a0a0ef1967e43fe66a234cf6..0d707d83911d518694455e15fbd1212aff609beb 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 37ea32f78db3e7ed2b712167f4a73cf9bd561579..97ee6df2ed2c7a840d0248450ebfef4a84197751 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)