def get_args():
args = argparse.ArgumentParser(description=get_desc())
args.add_argument("--reference", "-r", required=True, help="Path to reference file to prepare.")
args.add_argument("--mapper", help="Available mappers: %s" % available_mappers())
args.add_argument("--variant", help="Available variants: %s" % available_callers())
return args
def get_desc():
return r'''Run the snp pipeline with specified mapper, variant caller and some filters.
Available mappers: %s
Available variant callers: %s
Available filters: %s
Available annotators: %s''' % (available_mappers(), available_callers(), available_filters(), available_annotators())
def get_args():
args = argparse.ArgumentParser(description=get_desc())
args.add_argument("--reference",
"-r",
required=True,
help="Path to reference file to prepare.")
args.add_argument("--mapper",
help="Available mappers: %s" % available_mappers())
args.add_argument("--variant",
help="Available variants: %s" % available_callers())
return args
def get_args():
args = argparse.ArgumentParser(description=get_desc(),
formatter_class=RawTextHelpFormatter)
args.add_argument("--workflow", "-w")
args.add_argument("--input", "-i")
args.add_argument("-r1", help="R1/Forward read in Fastq format.")
args.add_argument("-r2", help="R2/Reverse read in Fastq format.")
args.add_argument("--reference",
"-r",
help="Rerefence to use for mapping.")
args.add_argument(
"--sample-name",
default="test_sample",
help="Name of the sample for mapper to include as read groups.")
args.add_argument("--outdir", "-o")
args.add_argument("--config", "-c")
args.add_argument("--mapper",
"-m",
default="bwa",
help="Available mappers: %s" % available_mappers())
args.add_argument("--mapper-options",
help="Custom maper options (advanced)")
args.add_argument("--bam")
args.add_argument("--variant",
"-v",
default="gatk",
help="Available variant callers: %s" %
available_callers())
args.add_argument("--variant-options",
help="Custom variant options (advanced)")
args.add_argument("--vcf")
args.add_argument(
"--filters",
type=str,
help=
"Filters to be applied to the VCF in key:value pairs, separated by comma (,). Available_filters: %s. Recommendations: GATK: mq_score:30,min_depth:10,ad_ratio:0.9 Mpileup: mq_score:30,min_depth:10,dp4_ratio:0.9"
% available_filters())
args.add_argument(
"--annotators",
nargs="+",
help="List of annotators to run before filters. Available: %s" %
available_annotators())
args.add_argument(
"--keep-temp",
action="store_true",
help="Keep intermediate files like BAMs and VCFs (default: False).")
args.add_argument(
"--json",
action="store_true",
help=
"Also write variant positions in filtered vcf as json file (default: False)."
)
args.add_argument(
"--json-info",
action="store_true",
help=
"When writing a json file, log some stats to stdout. (default: False)."
)
return args