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ex-291 (cgates): Increase rounding precision from 2 to 4 digits
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@cgates
cgates committed Sep 4, 2015
1 parent e005f36 commit dd6a20e
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Showing 25 changed files with 329 additions and 329 deletions.
4 changes: 2 additions & 2 deletions jacquard/utils/summarize_rollup_transform.py
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Original file line number Diff line number Diff line change
Expand Up @@ -66,12 +66,12 @@ def _get_non_null_values(record, sample, tag_type):

def _average(numeric_values):
average = str(sum(numeric_values)/Decimal(len(numeric_values)))
return utils.round_two_digits(average)
return utils.round_digits(average)

def _range(numeric_values):
if len(numeric_values) > 1:
value_range = str(max(numeric_values) - min(numeric_values))
return utils.round_two_digits(value_range)
return utils.round_digits(value_range)
return "."

def _count(numeric_values):
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2 changes: 1 addition & 1 deletion jacquard/utils/summarize_zscore_transform.py
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Expand Up @@ -135,7 +135,7 @@ def _zscore_as_str(zscore):
if zscore == ".":
return zscore
else:
return utils.round_two_digits(repr(zscore))
return utils.round_digits(repr(zscore))

def add_tag_values(self, vcf_record):
if not self._ok_to_add_tag_values(vcf_record):
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6 changes: 3 additions & 3 deletions jacquard/utils/utils.py
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Expand Up @@ -10,10 +10,10 @@


#TODO (cgates): Why does this need a string? Seems like it should take a number?
def round_two_digits(val):
def round_digits(val):
try:
if len(val.split(".")[1]) > 2:
return "{0:.2f}".format(float(val))
if len(val.split(".")[1]) > 4:
return "{0:.4f}".format(float(val))
except IndexError:
return val
return val
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2 changes: 1 addition & 1 deletion jacquard/variant_caller_transforms/mutect.py
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Expand Up @@ -56,7 +56,7 @@ def add_tag_values(self, vcf_record):
def _standardize_af(value):
new_values = []
for val in value:
new_values.append(utils.round_two_digits(val))
new_values.append(utils.round_digits(val))
return ",".join(new_values)

class _DepthTag(common_tags.AbstractJacquardTag):
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2 changes: 1 addition & 1 deletion jacquard/variant_caller_transforms/strelka.py
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Expand Up @@ -161,7 +161,7 @@ def add_tag_values(self, vcf_record):

@staticmethod
def _standardize_af(value):
return utils.round_two_digits(value)
return utils.round_digits(value)

class _DepthTag(common_tags.AbstractJacquardTag):
#pylint: disable=too-few-public-methods
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2 changes: 1 addition & 1 deletion jacquard/variant_caller_transforms/varscan.py
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Expand Up @@ -62,7 +62,7 @@ def _standardize_af(cls, value):
new_values = []
for val in value:
new_val = str(float(val.strip("%")) / 100)
new_values.append(utils.round_two_digits(new_val))
new_values.append(utils.round_digits(new_val))
return ",".join(new_values)

def __init__(self):
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80 changes: 40 additions & 40 deletions test/functional_tests/01_translate/benchmark/tiny.mutect.translatedTags.vcf
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34 changes: 17 additions & 17 deletions test/functional_tests/01_translate/benchmark/tiny.strelka.indels.translatedTags.vcf
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Expand Up @@ -3,7 +3,7 @@
##fileDate=20140709
##germlineIndelTheta=0.0001
##jacquard.translate.caller=Strelka
##jacquard=<timestamp="2015-05-15 14:42:14",command="<module 'jacquard.translate' from 'C:\Users\jebene\git\Jacquard\jacquard\translate.pyc'>",cwd="C:\Users\jebene\git">
##jacquard=<timestamp="2015-09-04 06:15:38",command="['translate', 'test/functional_tests/01_translate/input', 'test/functional_tests/01_translate/benchmark', '--force']",cwd="/Users/cgates/workspace",source="Jacquard",version="0.42">
##priorSomaticIndelRate=1e-06
##reference=file:ucsc.hg19.fasta
##source=strelka
Expand Down Expand Up @@ -69,22 +69,22 @@
##FORMAT=<ID=TIR,Number=2,Type=Integer,Description="Reads strongly supporting indel allele for tiers 1,2">
##FORMAT=<ID=TOR,Number=2,Type=Integer,Description="Other reads (weak support or insufficient indel breakpoint overlap) for tiers 1,2">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOR
chr1 721104 . TA T . QSI_ref;Repeat IC=8;IHP=11;NT=ref;QSI=6;QSI_NT=6;RC=9;RU=A;SGT=het->het;SOMATIC;TQSI=1;TQSI_NT=1 DP:DP2:TAR:TIR:TOR:DP50:FDP50:SUBDP50:JQ_SK_CALLER_REPORTED:JQ_SK_CALLER_PASSED:JQ_SK_AF:JQ_SK_DP:JQ_SK_HC_SOM:JQ_SK_GT 9:9:10,10:0,0:0,0:10.21:0.00:0.00:1:0:0.0:9:0:0/1 11:11:4,4:4,4:4,4:12.07:0.01:0.00:1:0:0.36:11:0:0/1
chr1 894535 . G GC . QSI_ref IC=6;IHP=5;NT=ref;QSI=8;QSI_NT=8;RC=5;RU=C;SGT=ref->het;SOMATIC;TQSI=1;TQSI_NT=1 DP:DP2:TAR:TIR:TOR:DP50:FDP50:SUBDP50:JQ_SK_CALLER_REPORTED:JQ_SK_CALLER_PASSED:JQ_SK_AF:JQ_SK_DP:JQ_SK_HC_SOM:JQ_SK_GT 12:12:10,10:0,0:2,2:10.57:0.00:0.00:1:0:0.0:12:0:0/0 13:13:7,7:3,3:3,3:11.37:0.33:0.00:1:0:0.23:13:0:0/1
chr1 1139982 . G GCC . QSI_ref IC=10;IHP=8;NT=ref;QSI=9;QSI_NT=9;RC=8;RU=C;SGT=ref->het;SOMATIC;TQSI=1;TQSI_NT=1 DP:DP2:TAR:TIR:TOR:DP50:FDP50:SUBDP50:JQ_SK_CALLER_REPORTED:JQ_SK_CALLER_PASSED:JQ_SK_AF:JQ_SK_DP:JQ_SK_HC_SOM:JQ_SK_GT 27:27:23,25:0,0:4,3:28.56:0.00:0.00:1:0:0.0:27:0:0/0 34:34:22,22:4,6:9,7:33.12:0.00:0.00:1:0:0.18:34:0:0/1
chr1 1333831 . GA G . Repeat IC=8;IHP=9;NT=ref;QSI=34;QSI_NT=34;RC=9;RU=A;SGT=ref->het;SOMATIC;TQSI=1;TQSI_NT=1 DP:DP2:TAR:TIR:TOR:DP50:FDP50:SUBDP50:JQ_SK_CALLER_REPORTED:JQ_SK_CALLER_PASSED:JQ_SK_AF:JQ_SK_DP:JQ_SK_HC_SOM:JQ_SK_GT 27:27:27,27:0,0:0,0:28.32:0.00:0.00:1:0:0.0:27:0:0/0 42:42:24,25:12,12:5,5:43.22:0.00:0.00:1:0:0.29:42:0:0/1
chr1 721104 . TA T . QSI_ref;Repeat IC=8;IHP=11;NT=ref;QSI=6;QSI_NT=6;RC=9;RU=A;SGT=het->het;SOMATIC;TQSI=1;TQSI_NT=1 DP:DP2:TAR:TIR:TOR:DP50:FDP50:SUBDP50:JQ_SK_CALLER_REPORTED:JQ_SK_CALLER_PASSED:JQ_SK_AF:JQ_SK_DP:JQ_SK_HC_SOM:JQ_SK_GT 9:9:10,10:0,0:0,0:10.21:0.00:0.00:1:0:0.0:9:0:0/1 11:11:4,4:4,4:4,4:12.07:0.01:0.00:1:0:0.3636:11:0:0/1
chr1 894535 . G GC . QSI_ref IC=6;IHP=5;NT=ref;QSI=8;QSI_NT=8;RC=5;RU=C;SGT=ref->het;SOMATIC;TQSI=1;TQSI_NT=1 DP:DP2:TAR:TIR:TOR:DP50:FDP50:SUBDP50:JQ_SK_CALLER_REPORTED:JQ_SK_CALLER_PASSED:JQ_SK_AF:JQ_SK_DP:JQ_SK_HC_SOM:JQ_SK_GT 12:12:10,10:0,0:2,2:10.57:0.00:0.00:1:0:0.0:12:0:0/0 13:13:7,7:3,3:3,3:11.37:0.33:0.00:1:0:0.2308:13:0:0/1
chr1 1139982 . G GCC . QSI_ref IC=10;IHP=8;NT=ref;QSI=9;QSI_NT=9;RC=8;RU=C;SGT=ref->het;SOMATIC;TQSI=1;TQSI_NT=1 DP:DP2:TAR:TIR:TOR:DP50:FDP50:SUBDP50:JQ_SK_CALLER_REPORTED:JQ_SK_CALLER_PASSED:JQ_SK_AF:JQ_SK_DP:JQ_SK_HC_SOM:JQ_SK_GT 27:27:23,25:0,0:4,3:28.56:0.00:0.00:1:0:0.0:27:0:0/0 34:34:22,22:4,6:9,7:33.12:0.00:0.00:1:0:0.1765:34:0:0/1
chr1 1333831 . GA G . Repeat IC=8;IHP=9;NT=ref;QSI=34;QSI_NT=34;RC=9;RU=A;SGT=ref->het;SOMATIC;TQSI=1;TQSI_NT=1 DP:DP2:TAR:TIR:TOR:DP50:FDP50:SUBDP50:JQ_SK_CALLER_REPORTED:JQ_SK_CALLER_PASSED:JQ_SK_AF:JQ_SK_DP:JQ_SK_HC_SOM:JQ_SK_GT 27:27:27,27:0,0:0,0:28.32:0.00:0.00:1:0:0.0:27:0:0/0 42:42:24,25:12,12:5,5:43.22:0.00:0.00:1:0:0.2857:42:0:0/1
chr1 1454460 . G GC . QSI_ref IC=5;IHP=5;NT=ref;QSI=10;QSI_NT=10;RC=4;RU=C;SGT=ref->het;SOMATIC;TQSI=1;TQSI_NT=1 DP:DP2:TAR:TIR:TOR:DP50:FDP50:SUBDP50:JQ_SK_CALLER_REPORTED:JQ_SK_CALLER_PASSED:JQ_SK_AF:JQ_SK_DP:JQ_SK_HC_SOM:JQ_SK_GT 13:13:10,11:0,0:3,2:12.89:0.00:0.00:1:0:0.0:13:0:0/0 20:20:15,15:4,4:1,1:17.61:0.26:0.00:1:0:0.2:20:0:0/1
chr1 1560350 . TG T . QSI_ref IC=6;IHP=7;NT=ref;QSI=20;QSI_NT=20;RC=7;RU=G;SGT=ref->het;SOMATIC;TQSI=1;TQSI_NT=1 DP:DP2:TAR:TIR:TOR:DP50:FDP50:SUBDP50:JQ_SK_CALLER_REPORTED:JQ_SK_CALLER_PASSED:JQ_SK_AF:JQ_SK_DP:JQ_SK_HC_SOM:JQ_SK_GT 22:22:19,21:0,0:3,3:24.04:0.76:0.00:1:0:0.0:22:0:0/0 44:44:30,30:10,10:4,4:40.73:0.40:0.00:1:0:0.23:44:0:0/1
chr1 1600084 . GT G . QSI_ref IC=7;IHP=11;NT=ref;QSI=9;QSI_NT=9;RC=8;RU=T;SGT=ref->het;SOMATIC;TQSI=1;TQSI_NT=1 DP:DP2:TAR:TIR:TOR:DP50:FDP50:SUBDP50:JQ_SK_CALLER_REPORTED:JQ_SK_CALLER_PASSED:JQ_SK_AF:JQ_SK_DP:JQ_SK_HC_SOM:JQ_SK_GT 47:47:43,45:2,2:3,3:47.18:0.00:0.00:1:0:0.04:47:0:0/0 69:69:37,41:18,18:14,15:68.37:0.00:0.00:1:0:0.26:69:0:0/1
chr1 1560350 . TG T . QSI_ref IC=6;IHP=7;NT=ref;QSI=20;QSI_NT=20;RC=7;RU=G;SGT=ref->het;SOMATIC;TQSI=1;TQSI_NT=1 DP:DP2:TAR:TIR:TOR:DP50:FDP50:SUBDP50:JQ_SK_CALLER_REPORTED:JQ_SK_CALLER_PASSED:JQ_SK_AF:JQ_SK_DP:JQ_SK_HC_SOM:JQ_SK_GT 22:22:19,21:0,0:3,3:24.04:0.76:0.00:1:0:0.0:22:0:0/0 44:44:30,30:10,10:4,4:40.73:0.40:0.00:1:0:0.2273:44:0:0/1
chr1 1600084 . GT G . QSI_ref IC=7;IHP=11;NT=ref;QSI=9;QSI_NT=9;RC=8;RU=T;SGT=ref->het;SOMATIC;TQSI=1;TQSI_NT=1 DP:DP2:TAR:TIR:TOR:DP50:FDP50:SUBDP50:JQ_SK_CALLER_REPORTED:JQ_SK_CALLER_PASSED:JQ_SK_AF:JQ_SK_DP:JQ_SK_HC_SOM:JQ_SK_GT 47:47:43,45:2,2:3,3:47.18:0.00:0.00:1:0:0.0426:47:0:0/0 69:69:37,41:18,18:14,15:68.37:0.00:0.00:1:0:0.2609:69:0:0/1
chr1 1606667 . C CG . QSI_ref IC=1;IHP=3;NT=ref;QSI=12;QSI_NT=12;RC=0;RU=G;SGT=ref->het;SOMATIC;TQSI=1;TQSI_NT=1 DP:DP2:TAR:TIR:TOR:DP50:FDP50:SUBDP50:JQ_SK_CALLER_REPORTED:JQ_SK_CALLER_PASSED:JQ_SK_AF:JQ_SK_DP:JQ_SK_HC_SOM:JQ_SK_GT 12:12:11,11:0,0:1,1:15.77:0.00:0.00:1:0:0.0:12:0:0/0 10:10:5,5:4,4:1,1:12.87:0.00:0.00:1:0:0.4:10:0:0/1
chr1 1633002 . G GC . QSI_ref IC=2;IHP=10;NT=ref;QSI=10;QSI_NT=10;RC=1;RU=C;SGT=ref->het;SOMATIC;TQSI=1;TQSI_NT=1 DP:DP2:TAR:TIR:TOR:DP50:FDP50:SUBDP50:JQ_SK_CALLER_REPORTED:JQ_SK_CALLER_PASSED:JQ_SK_AF:JQ_SK_DP:JQ_SK_HC_SOM:JQ_SK_GT 14:14:10,16:0,0:3,4:11.23:0.23:0.00:1:0:0.0:14:0:0/0 11:11:3,8:3,5:5,7:10.96:0.38:0.00:1:0:0.45:11:0:0/1
chr1 1663692 . AAAAG A . QSI_ref;iHpol IC=0;IHP=15;NT=ref;QSI=3;QSI_NT=3;RC=1;RU=AAAG;SGT=het->het;SOMATIC;TQSI=1;TQSI_NT=1 DP:DP2:TAR:TIR:TOR:DP50:FDP50:SUBDP50:JQ_SK_CALLER_REPORTED:JQ_SK_CALLER_PASSED:JQ_SK_AF:JQ_SK_DP:JQ_SK_HC_SOM:JQ_SK_GT 11:11:8,10:0,0:3,1:7.07:0.57:0.00:1:0:0.0:11:0:0/1 16:16:4,8:6,6:6,2:12.73:1.01:0.00:1:0:0.38:16:0:0/1
chr1 1688594 . G GC . QSI_ref IC=6;IHP=5;NT=ref;QSI=5;QSI_NT=5;RC=5;RU=C;SGT=ref->het;SOMATIC;TQSI=2;TQSI_NT=2 DP:DP2:TAR:TIR:TOR:DP50:FDP50:SUBDP50:JQ_SK_CALLER_REPORTED:JQ_SK_CALLER_PASSED:JQ_SK_AF:JQ_SK_DP:JQ_SK_HC_SOM:JQ_SK_GT 26:26:12,17:0,0:15,10:26.36:1.37:0.00:1:0:0.0:26:0:0/0 38:38:12,19:1,1:26,19:38.18:4.37:0.00:1:0:0.03:38:0:0/1
chr1 1696633 . GA G . PASS IC=7;IHP=9;NT=ref;QSI=33;QSI_NT=33;RC=8;RU=A;SGT=ref->het;SOMATIC;TQSI=2;TQSI_NT=2 DP:DP2:TAR:TIR:TOR:DP50:FDP50:SUBDP50:JQ_SK_CALLER_REPORTED:JQ_SK_CALLER_PASSED:JQ_SK_AF:JQ_SK_DP:JQ_SK_HC_SOM:JQ_SK_GT 48:48:46,46:0,0:2,2:44.73:0.00:0.00:1:1:0.0:48:0:0/0 45:45:28,28:12,12:6,6:47.86:0.00:0.00:1:1:0.27:45:1:0/1
chr1 1843532 . GC G . QSI_ref IC=7;IHP=8;NT=ref;QSI=23;QSI_NT=23;RC=8;RU=C;SGT=ref->het;SOMATIC;TQSI=1;TQSI_NT=1 DP:DP2:TAR:TIR:TOR:DP50:FDP50:SUBDP50:JQ_SK_CALLER_REPORTED:JQ_SK_CALLER_PASSED:JQ_SK_AF:JQ_SK_DP:JQ_SK_HC_SOM:JQ_SK_GT 24:24:21,23:0,0:4,2:22.25:0.00:0.00:1:0:0.0:24:0:0/0 33:33:22,22:8,8:3,3:29.35:0.17:0.00:1:0:0.24:33:0:0/1
chr1 1890704 . GT G . QSI_ref;Repeat IC=9;IHP=14;NT=ref;QSI=9;QSI_NT=9;RC=10;RU=T;SGT=ref->het;SOMATIC;TQSI=1;TQSI_NT=1 DP:DP2:TAR:TIR:TOR:DP50:FDP50:SUBDP50:JQ_SK_CALLER_REPORTED:JQ_SK_CALLER_PASSED:JQ_SK_AF:JQ_SK_DP:JQ_SK_HC_SOM:JQ_SK_GT 17:17:8,10:0,0:9,7:18.76:0.50:0.00:1:0:0.0:17:0:0/0 28:28:13,13:9,10:6,7:26.94:0.00:0.00:1:0:0.36:28:0:0/1
chr1 2002532 . AG A . QSI_ref IC=5;IHP=7;NT=ref;QSI=17;QSI_NT=17;RC=6;RU=G;SGT=ref->het;SOMATIC;TQSI=1;TQSI_NT=1 DP:DP2:TAR:TIR:TOR:DP50:FDP50:SUBDP50:JQ_SK_CALLER_REPORTED:JQ_SK_CALLER_PASSED:JQ_SK_AF:JQ_SK_DP:JQ_SK_HC_SOM:JQ_SK_GT 16:16:14,16:0,0:2,0:19.1:0.00:0.00:1:0:0.0:16:0:0/0 34:34:20,21:9,9:4,4:28.34:0.09:0.00:1:0:0.26:34:0:0/1
chr1 2118742 . CT C . QSI_ref;iHpol;Repeat IC=9;IHP=18;NT=ref;QSI=2;QSI_NT=2;RC=10;RU=T;SGT=ref->ref;SOMATIC;TQSI=1;TQSI_NT=1 DP:DP2:TAR:TIR:TOR:DP50:FDP50:SUBDP50:JQ_SK_CALLER_REPORTED:JQ_SK_CALLER_PASSED:JQ_SK_AF:JQ_SK_DP:JQ_SK_HC_SOM:JQ_SK_GT 20:20:11,12:0,0:10,9:22.42:0.73:0.00:1:0:0.0:20:0:0/0 29:29:15,17:5,6:8,6:30.74:0.44:0.00:1:0:0.21:29:0:0/0
chr1 2239135 . CT C . Repeat IC=8;IHP=12;NT=ref;QSI=33;QSI_NT=33;RC=9;RU=T;SGT=ref->het;SOMATIC;TQSI=1;TQSI_NT=1 DP:DP2:TAR:TIR:TOR:DP50:FDP50:SUBDP50:JQ_SK_CALLER_REPORTED:JQ_SK_CALLER_PASSED:JQ_SK_AF:JQ_SK_DP:JQ_SK_HC_SOM:JQ_SK_GT 47:47:37,39:1,1:9,9:44.15:0.14:0.00:1:0:0.02:47:0:0/0 99:99:52,56:27,27:21,18:95.2:0.84:0.00:1:0:0.27:99:0:0/1
chr1 1633002 . G GC . QSI_ref IC=2;IHP=10;NT=ref;QSI=10;QSI_NT=10;RC=1;RU=C;SGT=ref->het;SOMATIC;TQSI=1;TQSI_NT=1 DP:DP2:TAR:TIR:TOR:DP50:FDP50:SUBDP50:JQ_SK_CALLER_REPORTED:JQ_SK_CALLER_PASSED:JQ_SK_AF:JQ_SK_DP:JQ_SK_HC_SOM:JQ_SK_GT 14:14:10,16:0,0:3,4:11.23:0.23:0.00:1:0:0.0:14:0:0/0 11:11:3,8:3,5:5,7:10.96:0.38:0.00:1:0:0.4545:11:0:0/1
chr1 1663692 . AAAAG A . QSI_ref;iHpol IC=0;IHP=15;NT=ref;QSI=3;QSI_NT=3;RC=1;RU=AAAG;SGT=het->het;SOMATIC;TQSI=1;TQSI_NT=1 DP:DP2:TAR:TIR:TOR:DP50:FDP50:SUBDP50:JQ_SK_CALLER_REPORTED:JQ_SK_CALLER_PASSED:JQ_SK_AF:JQ_SK_DP:JQ_SK_HC_SOM:JQ_SK_GT 11:11:8,10:0,0:3,1:7.07:0.57:0.00:1:0:0.0:11:0:0/1 16:16:4,8:6,6:6,2:12.73:1.01:0.00:1:0:0.375:16:0:0/1
chr1 1688594 . G GC . QSI_ref IC=6;IHP=5;NT=ref;QSI=5;QSI_NT=5;RC=5;RU=C;SGT=ref->het;SOMATIC;TQSI=2;TQSI_NT=2 DP:DP2:TAR:TIR:TOR:DP50:FDP50:SUBDP50:JQ_SK_CALLER_REPORTED:JQ_SK_CALLER_PASSED:JQ_SK_AF:JQ_SK_DP:JQ_SK_HC_SOM:JQ_SK_GT 26:26:12,17:0,0:15,10:26.36:1.37:0.00:1:0:0.0:26:0:0/0 38:38:12,19:1,1:26,19:38.18:4.37:0.00:1:0:0.0263:38:0:0/1
chr1 1696633 . GA G . PASS IC=7;IHP=9;NT=ref;QSI=33;QSI_NT=33;RC=8;RU=A;SGT=ref->het;SOMATIC;TQSI=2;TQSI_NT=2 DP:DP2:TAR:TIR:TOR:DP50:FDP50:SUBDP50:JQ_SK_CALLER_REPORTED:JQ_SK_CALLER_PASSED:JQ_SK_AF:JQ_SK_DP:JQ_SK_HC_SOM:JQ_SK_GT 48:48:46,46:0,0:2,2:44.73:0.00:0.00:1:1:0.0:48:0:0/0 45:45:28,28:12,12:6,6:47.86:0.00:0.00:1:1:0.2667:45:1:0/1
chr1 1843532 . GC G . QSI_ref IC=7;IHP=8;NT=ref;QSI=23;QSI_NT=23;RC=8;RU=C;SGT=ref->het;SOMATIC;TQSI=1;TQSI_NT=1 DP:DP2:TAR:TIR:TOR:DP50:FDP50:SUBDP50:JQ_SK_CALLER_REPORTED:JQ_SK_CALLER_PASSED:JQ_SK_AF:JQ_SK_DP:JQ_SK_HC_SOM:JQ_SK_GT 24:24:21,23:0,0:4,2:22.25:0.00:0.00:1:0:0.0:24:0:0/0 33:33:22,22:8,8:3,3:29.35:0.17:0.00:1:0:0.2424:33:0:0/1
chr1 1890704 . GT G . QSI_ref;Repeat IC=9;IHP=14;NT=ref;QSI=9;QSI_NT=9;RC=10;RU=T;SGT=ref->het;SOMATIC;TQSI=1;TQSI_NT=1 DP:DP2:TAR:TIR:TOR:DP50:FDP50:SUBDP50:JQ_SK_CALLER_REPORTED:JQ_SK_CALLER_PASSED:JQ_SK_AF:JQ_SK_DP:JQ_SK_HC_SOM:JQ_SK_GT 17:17:8,10:0,0:9,7:18.76:0.50:0.00:1:0:0.0:17:0:0/0 28:28:13,13:9,10:6,7:26.94:0.00:0.00:1:0:0.3571:28:0:0/1
chr1 2002532 . AG A . QSI_ref IC=5;IHP=7;NT=ref;QSI=17;QSI_NT=17;RC=6;RU=G;SGT=ref->het;SOMATIC;TQSI=1;TQSI_NT=1 DP:DP2:TAR:TIR:TOR:DP50:FDP50:SUBDP50:JQ_SK_CALLER_REPORTED:JQ_SK_CALLER_PASSED:JQ_SK_AF:JQ_SK_DP:JQ_SK_HC_SOM:JQ_SK_GT 16:16:14,16:0,0:2,0:19.1:0.00:0.00:1:0:0.0:16:0:0/0 34:34:20,21:9,9:4,4:28.34:0.09:0.00:1:0:0.2647:34:0:0/1
chr1 2118742 . CT C . QSI_ref;iHpol;Repeat IC=9;IHP=18;NT=ref;QSI=2;QSI_NT=2;RC=10;RU=T;SGT=ref->ref;SOMATIC;TQSI=1;TQSI_NT=1 DP:DP2:TAR:TIR:TOR:DP50:FDP50:SUBDP50:JQ_SK_CALLER_REPORTED:JQ_SK_CALLER_PASSED:JQ_SK_AF:JQ_SK_DP:JQ_SK_HC_SOM:JQ_SK_GT 20:20:11,12:0,0:10,9:22.42:0.73:0.00:1:0:0.0:20:0:0/0 29:29:15,17:5,6:8,6:30.74:0.44:0.00:1:0:0.2069:29:0:0/0
chr1 2239135 . CT C . Repeat IC=8;IHP=12;NT=ref;QSI=33;QSI_NT=33;RC=9;RU=T;SGT=ref->het;SOMATIC;TQSI=1;TQSI_NT=1 DP:DP2:TAR:TIR:TOR:DP50:FDP50:SUBDP50:JQ_SK_CALLER_REPORTED:JQ_SK_CALLER_PASSED:JQ_SK_AF:JQ_SK_DP:JQ_SK_HC_SOM:JQ_SK_GT 47:47:37,39:1,1:9,9:44.15:0.14:0.00:1:0:0.0213:47:0:0/0 99:99:52,56:27,27:21,18:95.2:0.84:0.00:1:0:0.2727:99:0:0/1
chr1 2492901 . TCTC T . QSI_ref IC=1;IHP=4;NT=ref;QSI=19;QSI_NT=19;RC=2;RU=CTC;SGT=ref->het;SOMATIC;TQSI=1;TQSI_NT=1 DP:DP2:TAR:TIR:TOR:DP50:FDP50:SUBDP50:JQ_SK_CALLER_REPORTED:JQ_SK_CALLER_PASSED:JQ_SK_AF:JQ_SK_DP:JQ_SK_HC_SOM:JQ_SK_GT 23:23:22,23:0,0:2,2:27.84:0.00:0.00:1:0:0.0:23:0:0/0 30:30:21,21:6,6:4,4:31.06:0.00:0.00:1:0:0.2:30:0:0/1
chr1 2704027 . AC A . QSI_ref IC=5;IHP=7;NT=ref;QSI=21;QSI_NT=21;RC=6;RU=C;SGT=ref->het;SOMATIC;TQSI=1;TQSI_NT=1 DP:DP2:TAR:TIR:TOR:DP50:FDP50:SUBDP50:JQ_SK_CALLER_REPORTED:JQ_SK_CALLER_PASSED:JQ_SK_AF:JQ_SK_DP:JQ_SK_HC_SOM:JQ_SK_GT 17:17:16,17:0,0:1,0:17.73:0.00:0.00:1:0:0.0:17:0:0/0 22:22:14,14:8,8:1,1:19.77:0.00:0.00:1:0:0.36:22:0:0/1
chr1 2704027 . AC A . QSI_ref IC=5;IHP=7;NT=ref;QSI=21;QSI_NT=21;RC=6;RU=C;SGT=ref->het;SOMATIC;TQSI=1;TQSI_NT=1 DP:DP2:TAR:TIR:TOR:DP50:FDP50:SUBDP50:JQ_SK_CALLER_REPORTED:JQ_SK_CALLER_PASSED:JQ_SK_AF:JQ_SK_DP:JQ_SK_HC_SOM:JQ_SK_GT 17:17:16,17:0,0:1,0:17.73:0.00:0.00:1:0:0.0:17:0:0/0 22:22:14,14:8,8:1,1:19.77:0.00:0.00:1:0:0.3636:22:0:0/1
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