Wrong summary statistic file

Hail Query & hailctl
1

I get the wrong summary statistic file. The following is my code. I don’t know if there is any mistakes in my pipeline.

contig = "autosomes"
pipeline = 0

if contig == 'autosomes':
    contig_expr = 'c{1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22}'
else:
    contig_expr = contig

if contig not in set(['autosomes', 'chrX', 'chrXY']):
    raise ValueError(f'Invalid contig argument "{contig}" - must be one of {{"autosomes", "chrX", "chrXY"}}.')


ht_phenotypes = hl.read_table(project_path + f'data/processed/biomarker/biomarkers_gwas.pipeline_{pipeline}.ht')
ht_covariates = hl.read_table(project_path + f"data/processed/biomarker/gwas_covariates.ht")
ht_variants = hl.import_table(project_path + f'data/raw/gene/variants.tsv', impute=True, missing="")
ht_variants = ht_variants.annotate(variant = hl.parse_variant(ht_variants.variant))

mt = hl.import_bgen(
    path=project_path+ f'data/raw/gene/bgen/ukb_{contig_expr}_b0_v3.bgen',
    sample_file=project_path+ f'data/raw/gene/sample/{contig}.sample',
    entry_fields=['dosage'],
    variants=ht_variants.variant)

mt = mt.annotate_cols(
    phenotypes=ht_phenotypes[mt.s],
    covariates=ht_covariates[mt.s])

phenotypes = list(mt['phenotypes'].keys())
print(phenotypes)

ht = hl.linear_regression_rows(
    y=[[mt['phenotypes'][y]] for y in phenotypes],
    x=mt.dosage,
    covariates=[1, *[mt['covariates'][x] for x in list(mt['covariates'].keys())]],
    pass_through=['varid', 'rsid'])

ht = ht.annotate_globals(phenotypes=phenotypes)

ht.write(project_path + f"data/processed/gwas/biomarker_gwas_results.{contig}.pipeline_{pipeline}.ht",
         overwrite=True)

Thanks,
Meng

2

I found that the P column of summary statistic have NaN value. I don’t know why this happened and how can I get rid of it.

3

I want to know whether hail can handle cases where the phenotype has NA.