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Associatr add --beagle-dosages flag #20

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ddf4ff3
add --beagle-dosages flag
nicholema Aug 15, 2024
0bdf58f
add --beagle-dosages in readme
nicholema Aug 15, 2024
fd968b6
add --beagle-dosages in readme
nicholema Aug 15, 2024
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1 change: 1 addition & 0 deletions gwas/aou/README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -54,6 +54,7 @@ Optional arguments:
* `--MAF`: Apply minor allele frequency QC. Default=0.01
* `--HWE`: Apply HWE p-value cutoff QC. Default=1e-15
* `--GQ`: Apply minimun genotype score QC. Default=20
* `--beagle-dosages`: Apply beagle dosages flag to associaTR. Default=false


## Important file locations:
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3 changes: 2 additions & 1 deletion gwas/aou/aou_gwas.py
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Expand Up @@ -110,6 +110,7 @@ def main():
parser.add_argument("--MAF", help="Apply minor allele frequency QC", type=float, default=0.01)
parser.add_argument("--HWE", help="Apply HWE p-value cutoff QC", type=float, default=1e-100)
parser.add_argument("--GQ", help="Apply minimun genotype score QC", type=int, default=20)
parser.add_argument("--beagle-dosages", help="Apply beagle dosages flag to associaTR ,Default: False",action="store_true")
args = parser.parse_args()

# Set up paths
Expand Down Expand Up @@ -185,7 +186,7 @@ def main():
runner = HailRunner(data, region=args.region, covars=covars, sample_call_rate=args.sample_call_rate, variant_call_rate=args.variant_call_rate, MAF=args.MAF, HWE=args.HWE, GQ=args.GQ)
elif args.method == "associaTR":
from associatr_runner import AssociaTRRunner
runner = AssociaTRRunner(data, args.tr_vcf, region=args.region, covars=covars)
runner = AssociaTRRunner(data, args.tr_vcf, region=args.region, covars=covars, beagle=args.beagle_dosages)
else:
ERROR("GWAS method %s not implemented" % args.method)

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7 changes: 4 additions & 3 deletions gwas/aou/associatr_runner.py
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Expand Up @@ -9,13 +9,14 @@
import trtools.associaTR

class AssociaTRRunner:
def __init__(self, ptcovar, trvcf, region=None, covars=[]):
def __init__(self, ptcovar, trvcf, beagle, region=None, covars=[]):
self.ptcovar = ptcovar
self.pt_npy = None
self.covar_npy = None
self.trvcf = trvcf
self.region = region
self.covars = covars
self.beagle = beagle
self.gwas = None
self.method = "associaTR"
self.setup()
Expand All @@ -42,7 +43,7 @@ def RunGWAS(self):
same_samples = False
sample_list = None
non_major_cutoff = 20
beagle_dosages = False
#beagle_dosages = False
plotting_phenotype = None
paired_genotype_plot = False
plot_genotype_residuals = False
Expand All @@ -59,7 +60,7 @@ def RunGWAS(self):
sample_list,
self.region,
non_major_cutoff,
beagle_dosages,
self.beagle,
plotting_phenotype,
paired_genotype_plot,
plot_genotype_residuals,
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