def validate(self, vcf_path, plot=False, king=False):
if king:
from .king import run_king
run_king(vcf_path, self)
else:
from cyvcf2 import VCF
vcf = VCF(vcf_path, gts012=True, lazy=True)
rels = list(
vcf.relatedness(min_af=0.02,
n_variants=39000,
gap=10000,
linkage_max=1.5))
if plot:
fig = vcf.plot_relatedness(rels[:])
fig.show()
fig.savefig('t.png')
print("sample_1\tsample_2\tped_relation\tvcf_relation\trel\tIBS")
for rel in rels:
sample_a, sample_b = rel['pair']
ped_rel = self.relation(sample_a, sample_b)
if ped_rel is None: continue
out_line = "%s\t%s\t%s\t%s\t%.2f\t%.3f" % (
sample_a, sample_b, ped_rel, "|".join(
rel['tags']), rel['rel'], rel['ibs'])
if rel['rel'] < 0.04: # likely unrelated
if ped_rel not in ('related level 2', 'unrelated'):
print(out_line)
continue
if rel['rel'] < 0.15:
if ped_rel not in ('unrelated', 'related level 2',
'distant relations'):
print(out_line)
continue
if 0.26 < rel['rel'] < 0.78:
if ped_rel not in ('parent-child', 'full siblings'):
print(out_line)
continue
if 0.15 < rel['rel'] < 0.3:
if ped_rel not in ('related level 2', 'unrelated'):
print(out_line)
continue
if ped_rel > 0.78:
if ped_rel not in ('identical twins', 'self'):
print(out_line)
continue
def validate(self, vcf_path, plot=False, king=False):
if king:
from .king import run_king
run_king(vcf_path, self)
else:
from cyvcf2 import VCF
vcf = VCF(vcf_path, gts012=True, lazy=True)
rels = list(vcf.relatedness(min_af=0.02, n_variants=39000, gap=10000, linkage_max=1.5))
if plot:
fig = vcf.plot_relatedness(rels[:])
fig.show()
fig.savefig('t.png')
print("sample_1\tsample_2\tped_relation\tvcf_relation\trel\tIBS")
for rel in rels:
sample_a, sample_b = rel['pair']
ped_rel = self.relation(sample_a, sample_b)
if ped_rel is None: continue
out_line = "%s\t%s\t%s\t%s\t%.2f\t%.3f" % (sample_a, sample_b,
ped_rel, "|".join(rel['tags']), rel['rel'], rel['ibs'])
if rel['rel'] < 0.04: # likely unrelated
if ped_rel not in ('related level 2', 'unrelated'):
print(out_line)
continue
if rel['rel'] < 0.15:
if ped_rel not in ('unrelated', 'related level 2', 'distant relations'):
print(out_line)
continue
if 0.26 < rel['rel'] < 0.78:
if ped_rel not in ('parent-child', 'full siblings'):
print(out_line)
continue
if 0.15 < rel['rel'] < 0.3:
if ped_rel not in ('related level 2', 'unrelated'):
print(out_line)
continue
if ped_rel > 0.78:
if ped_rel not in ('identical twins', 'self'):
print(out_line)
continue
