Commit e6309163 authored by van den Berg's avatar van den Berg
Browse files

The discordant VCF file is gzipped

parent e62c9164
Pipeline #2865 failed with stage
in 21 seconds
......@@ -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.
......
......@@ -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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