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Klinische Genetica
capture-lumc
vtools
Commits
c76505da
Commit
c76505da
authored
Nov 12, 2019
by
van den Berg
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Merge branch 'testing' of git.lumc.nl:klinische-genetica/capture-lumc/vtools into testing
parents
d37115cc
955802ec
Pipeline
#2786
failed with stage
in 23 seconds
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tests/cases/gatk_no_alt.vcf.gz
tests/cases/gatk_no_alt.vcf.gz
+0
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tests/cases/gatk_no_alt.vcf.gz.tbi
tests/cases/gatk_no_alt.vcf.gz.tbi
+0
-0
tests/test_evaluate.py
tests/test_evaluate.py
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tests/cases/gatk_no_alt.vcf.gz
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tests/test_evaluate.py
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...
...
@@ -393,3 +393,51 @@ def test_known_concordant_RGQ_min_qc_100():
positive_samples
=
[
'NA12878'
],
min_gq
=
100
,
min_dp
=
0
)
assert
d
[
'alleles_hom_ref_concordant'
]
==
0
@
pytest
.
fixture
(
scope
=
'module'
)
def
gatk_no_alt_in_call
():
""" Test statistics when the ALT allele is missing from the called vcf
The ALT allele has been set to '.' for each variant, and the corresponding
GT has been set to 0/0 to generate valid variants.
"""
filename
=
'tests/cases/gatk.vcf.gz'
no_alt
=
'tests/cases/gatk_no_alt.vcf.gz'
positive
=
VCF
(
filename
,
gts012
=
True
)
call
=
VCF
(
no_alt
,
gts012
=
True
)
d
,
disc
=
site_concordancy
(
call
,
positive
,
call_samples
=
[
'BLANK'
],
positive_samples
=
[
'BLANK'
],
min_dp
=
0
,
min_gq
=
0
)
return
d
def
test_no_alt_call_total_sites
(
gatk_no_alt_in_call
):
assert
gatk_no_alt_in_call
[
'total_sites'
]
==
37
def
test_no_alt_call_sites_considered
(
gatk_no_alt_in_call
):
assert
gatk_no_alt_in_call
[
'sites_considered'
]
==
37
def
test_no_alt_call_het_concordant
(
gatk_no_alt_in_call
):
assert
gatk_no_alt_in_call
[
'alleles_het_concordant'
]
==
0
def
test_no_alt_call_hom_alt_concordant
(
gatk_no_alt_in_call
):
assert
gatk_no_alt_in_call
[
'alleles_hom_alt_concordant'
]
==
0
def
test_no_alt_call_hom_ref_concordant
(
gatk_no_alt_in_call
):
assert
gatk_no_alt_in_call
[
'alleles_hom_ref_concordant'
]
==
32
def
test_no_alt_call_alleles_concordant
(
gatk_no_alt_in_call
):
assert
gatk_no_alt_in_call
[
'alleles_concordant'
]
==
46
def
test_no_alt_call_alleles_discordant
(
gatk_no_alt_in_call
):
assert
gatk_no_alt_in_call
[
'alleles_discordant'
]
==
20
def
test_no_alt_call_alleles_no_call
(
gatk_no_alt_in_call
):
assert
gatk_no_alt_in_call
[
'alleles_no_call'
]
==
8
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