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ex-262 (jebene/dkriti) - added strelka genotype
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@jebene
jebene committed May 15, 2015
1 parent 2702f69 commit 407b0ab
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Showing 12 changed files with 315 additions and 160 deletions.
49 changes: 24 additions & 25 deletions jacquard/variant_caller_transforms/mutect.py
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Original file line number Diff line number Diff line change
Expand Up @@ -11,6 +11,30 @@
JQ_MUTECT_TAG = "JQ_MT_"
VERSION = "v1.1.4"

class _GenotypeTag(object):
#pylint: disable=too-few-public-methods
@classmethod
def _standardize_gt(cls, value):
if value == "0":
value = "0/0"
return value

def __init__(self):
self.metaheader = ('##FORMAT=<ID={0}GT,'
'Number=1,'
'Type=String,'
'Description="Jacquard genotype (based on GT)">')\
.format(JQ_MUTECT_TAG)

@staticmethod
def add_tag_values(vcf_record):
if "GT" in vcf_record.format_tags:
sample_values = {}
for samp in vcf_record.sample_tag_values:
genotype = vcf_record.sample_tag_values[samp]["GT"]
sample_values[samp] = _GenotypeTag._standardize_gt(genotype)
vcf_record.add_sample_tag_value(JQ_MUTECT_TAG + "GT", sample_values)

class _AlleleFreqTag(object):
#pylint: disable=too-few-public-methods
def __init__(self):
Expand All @@ -36,31 +60,6 @@ def _standardize_af(value):
new_values.append(utils.round_two_digits(val))
return ",".join(new_values)

class _GenotypeTag(object):
#pylint: disable=too-few-public-methods
@classmethod
def _standardize_gt(cls, value):
if value == "0":
value = "0/0"
return value

def __init__(self):
self.metaheader = ('##FORMAT=<ID={0}GT,'
'Number=1,'
'Type=String,'
#pylint: disable=line-too-long
'Description="Jacquard genotype (based on GT)">')\
.format(JQ_MUTECT_TAG)

@staticmethod
def add_tag_values(vcf_record):
if "GT" in vcf_record.format_tags:
sample_values = {}
for samp in vcf_record.sample_tag_values:
genotype = vcf_record.sample_tag_values[samp]["GT"]
sample_values[samp] = _GenotypeTag._standardize_gt(genotype)
vcf_record.add_sample_tag_value(JQ_MUTECT_TAG + "GT", sample_values)

class _DepthTag(object):
#pylint: disable=too-few-public-methods
def __init__(self):
Expand Down
60 changes: 59 additions & 1 deletion jacquard/variant_caller_transforms/strelka.py
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Original file line number Diff line number Diff line change
Expand Up @@ -24,6 +24,63 @@
JQ_STRELKA_TAG = "JQ_SK_"
VERSION = "v2.0.15"

class _GenotypeTag(object):
_INDEL_VALUES = ["ref", "hom", "het"]

def __init__(self):
#pylint: disable=line-too-long
self.metaheader = ('##FORMAT=<ID={}GT,'
'Number=1,'
'Type=String,'
'Description="Jacquard genotype (based on SGT). Example for snv: REF=A, ALT=C, INFO:SGT=AA->AC is translated as normal=0/0, tumor=0/1. Example for indel: INFO:SGT=ref->het is translated as normal=0/0, tumor=0/1.">')\
.format(JQ_STRELKA_TAG)

@staticmethod
def _get_indel_genotype(sample_genotype):
indel_mapping_values = {"ref":"0/0","het":"0/1","hom":"1/1"}
if sample_genotype in indel_mapping_values:
return indel_mapping_values[sample_genotype]
else:
raise utils.JQException("Unable to determine Genotype")

@staticmethod
def _get_snv_genotype(sample_genotype, ref, alt):
sample_allele1, sample_allele2 = list(sample_genotype)
alleles = [ref]
alleles.extend(alt.split(","))

numerator = None
denominator = None

for i, allele in enumerate(alleles):
if sample_allele1 == allele:
numerator = str(i)
if sample_allele2 == allele:
denominator = str(i)

if numerator and denominator:
return numerator+"/"+denominator
else:
raise utils.JQException("Unable to determine Genotype")

def add_tag_values(self, vcf_record):
sample_values = {}
if "SGT" in vcf_record.info_dict:
sample_genotypes = vcf_record.info_dict["SGT"].split("->")

for i, sample in enumerate(vcf_record.sample_tag_values):
if sample_genotypes[i] in _GenotypeTag._INDEL_VALUES:
genotype = self._get_indel_genotype(sample_genotypes[i])
else:
genotype = self._get_snv_genotype(sample_genotypes[i],
vcf_record.ref,
vcf_record.alt)
sample_values[sample] = genotype

if sample_values:
vcf_record.add_sample_tag_value(JQ_STRELKA_TAG + "GT",
sample_values)

class _AlleleFreqTag(object):
#pylint: disable=too-few-public-methods
def __init__(self):
Expand Down Expand Up @@ -272,7 +329,8 @@ def __init__(self, vcf_reader):
common_tags.PassedTag(JQ_STRELKA_TAG),
_AlleleFreqTag(),
_DepthTag(),
_SomaticTag()]
_SomaticTag(),
_GenotypeTag()]

def _get_new_metaheaders(self):
return [tag.metaheader for tag in self.tags]
Expand Down
1 change: 1 addition & 0 deletions jacquard/variant_caller_transforms/varscan.py
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Original file line number Diff line number Diff line change
Expand Up @@ -35,6 +35,7 @@
VERSION = "v2.3"

class _GenotypeTag(object):
#pylint: disable=too-few-public-methods
def __init__(self):
self.metaheader = ('##FORMAT=<ID={0}GT,'
'Number=1,'
Expand Down
41 changes: 21 additions & 20 deletions test/functional_tests/01_translate/benchmark/tiny.strelka.indels.translatedTags.vcf
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Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@
##fileDate=20140709
##germlineIndelTheta=0.0001
##jacquard.translate.caller=Strelka
##jacquard=<Timestamp="2015-05-15 11:52:10",Command="<module 'jacquard.translate' from 'C:\Users\jebene\git\Jacquard\jacquard\translate.pyc'>",Cwd="C:\Users\jebene\git">
##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">
##priorSomaticIndelRate=1e-06
##reference=file:ucsc.hg19.fasta
##source=strelka
Expand Down Expand Up @@ -62,28 +62,29 @@
##FORMAT=<ID=JQ_SK_CALLER_PASSED,Number=1,Type=Integer,Description="1 = variant FILTER is PASS in original VCF">
##FORMAT=<ID=JQ_SK_CALLER_REPORTED,Number=1,Type=Integer,Description="1 = variant present in original VCF">
##FORMAT=<ID=JQ_SK_DP,Number=1,Type=Float,Description="Jacquard depth for Strelka (uses DP2 if available, otherwise uses ACGT tier2 depth)">
##FORMAT=<ID=JQ_SK_GT,Number=1,Type=String,Description="Jacquard genotype (based on SGT). Example for snv: REF=A, ALT=C, INFO:SGT=AA->AC is translated as normal=0/0, tumor=0/1. Example for indel: INFO:SGT=ref->het is translated as normal=0/0, tumor=0/1.">
##FORMAT=<ID=JQ_SK_HC_SOM,Number=1,Type=Integer,Description="Jacquard somatic status for Strelka: 0=non-somatic,1=somatic (based on PASS in FILTER column)">
##FORMAT=<ID=SUBDP50,Number=1,Type=Float,Description="Average number of reads below tier1 mapping quality threshold aligned across sites within 50 bases">
##FORMAT=<ID=TAR,Number=2,Type=Integer,Description="Reads strongly supporting alternate allele for tiers 1,2">
##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 9:9:10,10:0,0:0,0:10.21:0.00:0.00:1:0:0.0:9:0 11:11:4,4:4,4:4,4:12.07:0.01:0.00:1:0:0.36:11:0
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 12:12:10,10:0,0:2,2:10.57:0.00:0.00:1:0:0.0:12:0 13:13:7,7:3,3:3,3:11.37:0.33:0.00:1:0:0.23:13:0
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 27:27:23,25:0,0:4,3:28.56:0.00:0.00:1:0:0.0:27:0 34:34:22,22:4,6:9,7:33.12:0.00:0.00:1:0:0.18:34:0
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 27:27:27,27:0,0:0,0:28.32:0.00:0.00:1:0:0.0:27:0 42:42:24,25:12,12:5,5:43.22:0.00:0.00:1:0:0.29:42:0
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 13:13:10,11:0,0:3,2:12.89:0.00:0.00:1:0:0.0:13:0 20:20:15,15:4,4:1,1:17.61:0.26:0.00:1:0:0.2:20:0
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 22:22:19,21:0,0:3,3:24.04:0.76:0.00:1:0:0.0:22:0 44:44:30,30:10,10:4,4:40.73:0.40:0.00:1:0:0.23:44:0
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 47:47:43,45:2,2:3,3:47.18:0.00:0.00:1:0:0.04:47:0 69:69:37,41:18,18:14,15:68.37:0.00:0.00:1:0:0.26:69:0
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 12:12:11,11:0,0:1,1:15.77:0.00:0.00:1:0:0.0:12:0 10:10:5,5:4,4:1,1:12.87:0.00:0.00:1:0:0.4:10:0
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 14:14:10,16:0,0:3,4:11.23:0.23:0.00:1:0:0.0:14:0 11:11:3,8:3,5:5,7:10.96:0.38:0.00:1:0:0.45:11:0
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 11:11:8,10:0,0:3,1:7.07:0.57:0.00:1:0:0.0:11:0 16:16:4,8:6,6:6,2:12.73:1.01:0.00:1:0:0.38:16:0
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 26:26:12,17:0,0:15,10:26.36:1.37:0.00:1:0:0.0:26:0 38:38:12,19:1,1:26,19:38.18:4.37:0.00:1:0:0.03:38:0
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 48:48:46,46:0,0:2,2:44.73:0.00:0.00:1:1:0.0:48:0 45:45:28,28:12,12:6,6:47.86:0.00:0.00:1:1:0.27:45:1
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 24:24:21,23:0,0:4,2:22.25:0.00:0.00:1:0:0.0:24:0 33:33:22,22:8,8:3,3:29.35:0.17:0.00:1:0:0.24:33:0
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 17:17:8,10:0,0:9,7:18.76:0.50:0.00:1:0:0.0:17:0 28:28:13,13:9,10:6,7:26.94:0.00:0.00:1:0:0.36:28:0
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 16:16:14,16:0,0:2,0:19.1:0.00:0.00:1:0:0.0:16:0 34:34:20,21:9,9:4,4:28.34:0.09:0.00:1:0:0.26:34:0
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 20:20:11,12:0,0:10,9:22.42:0.73:0.00:1:0:0.0:20:0 29:29:15,17:5,6:8,6:30.74:0.44:0.00:1:0:0.21:29:0
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 47:47:37,39:1,1:9,9:44.15:0.14:0.00:1:0:0.02:47:0 99:99:52,56:27,27:21,18:95.2:0.84:0.00:1:0:0.27:99:0
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 23:23:22,23:0,0:2,2:27.84:0.00:0.00:1:0:0.0:23:0 30:30:21,21:6,6:4,4:31.06:0.00:0.00:1:0:0.2:30:0
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 17:17:16,17:0,0:1,0:17.73:0.00:0.00:1:0:0.0:17:0 22:22:14,14:8,8:1,1:19.77:0.00:0.00:1:0:0.36:22:0
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 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 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 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
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