def parse_args(ARGS):
args = argparse.ArgumentParser()
import vcfscreen.arguments as a
args = a.args_vars(args)
args = a.args_annots(args)
args = a.args_phredthresh(args,
sampletypes=[""],
gt_types=["homref", "het", "homalt"],
threshes=["max", "min"])
args = a.args_perc_alt(args, sampletypes=[""], threshes=["max", "min"])
args = a.args_cnds(args, variant_cnds=True, sampletypes=["gt"])
args = a.args_req(args)
return args.parse_args(args=ARGS)
def parse_args(ARGS):
args = argparse.ArgumentParser()
import vcfscreen.arguments as a
args = a.args_vars(args)
args = a.args_annots(args)
args.add_argument("--annotation-subfield",
type=str,
default="CSQ",
help="annotation subfield string to use")
args.add_argument("variant_cnds", help="input vcf file")
args.add_argument("in_vcf", help="input vcf file")
args.add_argument("out_vcf", help="output vcf file.")
return args.parse_args(args=ARGS)
def parse_args(ARGS):
args = argparse.ArgumentParser()
import vcfscreen.arguments as a
args = a.args_vars(args)
args = a.args_annots(args)
args = a.args_phredthresh(args,
sampletypes=["pro","transpar", "ntranspar"],
gt_types=["homref","het","homalt"],
threshes=["max","min"])
args = a.args_perc_alt(args,
sampletypes=["pro","transpar","ntranspar"],
threshes=["max","min"])
args = a.args_cnds(args, variant_cnds=True,
sampletypes=["pro","transpar","ntranspar"])
args.add_argument("--ntrans",
action="store_true", default=False,
help="instead of looking for parental transmitted vars, " +\
"look for nontransmitted variants.")
args = a.args_req(args)
return args.parse_args(args=ARGS)
def parse_args(ARGS):
args = argparse.ArgumentParser()
import vcfscreen.arguments as a
args = a.args_vars(args)
args = a.args_annots(args)
args = a.args_phredthresh(args,
sampletypes=["iid", "pid", "mid"],
gt_types=["hom", "het"],
threshes=["max", "min"])
args = a.args_perc_alt(args,
sampletypes=["iid", "pid", "mid"],
threshes=["max", "min"])
args = a.args_cnds(args,
variant_cnds=True,
sampletypes=["iid", "pid", "mid"])
args.add_argument("--x-chrom-interval",
type=str,
action="store",
default="X:1-155270560",
help="span of X chromosome to screen.")
args = a.args_req(args)
return args.parse_args(args=ARGS)