ex-260 (jebene/dkriti) added varscan genotype tags

jacquard/variant_caller_transforms/varscan.py

@@ -34,6 +34,24 @@
 JQ_VARSCAN_TAG = "JQ_VS_"
 VERSION = "v2.3"
 
+class _GenotypeTag(object):
+    def __init__(self):
+        self.metaheader = ('##FORMAT=<ID={0}GT,'
+                           'Number=1,'
+                           'Type=String,'
+                           'Description="Jacquard genotype (based on GT)">')\
+                           .format(JQ_VARSCAN_TAG)
+
+    @staticmethod
+    def add_tag_values(vcf_record):
+        sample_values = {}
+        if "GT" in vcf_record.format_tags:
+            for sample in vcf_record.sample_tag_values:
+                genotype = vcf_record.sample_tag_values[sample]["GT"]
+                sample_values[sample] = genotype
+            vcf_record.add_sample_tag_value(JQ_VARSCAN_TAG + "GT",
+                                            sample_values)
+
 class _AlleleFreqTag(object):
     #pylint: disable=too-few-public-methods
     @classmethod
@@ -427,7 +445,8 @@ def __init__(self, vcf_reader, som_hc_file_reader=None):
                      common_tags.PassedTag(JQ_VARSCAN_TAG),
                      _AlleleFreqTag(),
                      _DepthTag(),
-                     _SomaticTag()]
+                     _SomaticTag(),
+                     _GenotypeTag()]
 
         if som_hc_file_reader:
             self.tags.insert(0, _HCTag(som_hc_file_reader))

test/functional_tests/01_translate/benchmark/tiny.mutect.translatedTags.vcf

@@ -1,7 +1,7 @@
 ##fileformat=VCFv4.1
 ##MuTect="analysis_type=MuTect input_file=[11N_25714.sorted.bam, 11Ta_25715.sorted.bam] read_buffer_size=null phone_home=STANDARD gatk_key=null tag=NA read_filter=[BadCigar] intervals=[TargetRegion_buffered10bases.bed] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=ucsc.hg19.fasta nonDeterministicRandomSeed=false disableRandomization=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 enable_experimental_downsampling=false baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 defaultBaseQualities=-1 validation_strictness=SILENT remove_program_records=false keep_program_records=false unsafe=null num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false logging_level=INFO log_to_file=null help=false noop=false enable_extended_output=false artifact_detection_mode=false tumor_sample_name=25715 bam_tumor_sample_name=null normal_sample_name=25714 force_output=false force_alleles=false only_passing_calls=false initial_tumor_lod=4.0 tumor_lod=6.3 fraction_contamination=0.02 minimum_mutation_cell_fraction=0.0 normal_lod=2.2 normal_artifact_lod=1.0 strand_artifact_lod=2.0 strand_artifact_power_threshold=0.9 dbsnp_normal_lod=5.5 somatic_classification_normal_power_threshold=0.95 minimum_normal_allele_fraction=0.0 tumor_f_pretest=0.0050 min_qscore=5 gap_events_threshold=3 heavily_clipped_read_fraction=0.3 clipping_bias_pvalue_threshold=0.05 fraction_mapq0_threshold=0.5 pir_median_threshold=10.0 pir_mad_threshold=3.0 required_maximum_alt_allele_mapping_quality_score=20 max_alt_alleles_in_normal_count=2 max_alt_alleles_in_normal_qscore_sum=20 max_alt_allele_in_normal_fraction=0.03 power_constant_qscore=30 absolute_copy_number_data=null power_constant_af=0.30000001192092896 vcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub dbsnp=[(RodBinding name=dbsnp source=dbsnp_138.hg19.vcf)] cosmic=[(RodBinding name=cosmic source=Cosmic.v68.hg19.vcf)] normal_panel=[] coverage_20_q20_file=null power_file=null tumor_depth_file=null normal_depth_file=null filter_mismatching_base_and_quals=false"
 ##jacquard.translate.caller=MuTect
-##jacquard=<Timestamp="2015-03-30 13:30:01",Command="<module 'jacquard.translate' from 'C:\Users\jebene\git\Jacquard\jacquard\translate.pyc'>",Cwd="C:\Users\jebene\git">
+##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">
 ##reference=file:ucsc.hg19.fasta
 ##contig=<ID=chr1,length=249250621,assembly=hg19>
 ##contig=<ID=chr1_gl000191_random,length=106433,assembly=hg19>

test/functional_tests/01_translate/benchmark/tiny.strelka.indels.translatedTags.vcf

@@ -3,7 +3,7 @@
 ##fileDate=20140709
 ##germlineIndelTheta=0.0001
 ##jacquard.translate.caller=Strelka
-##jacquard=<Timestamp="2015-03-30 13:30:01",Command="<module 'jacquard.translate' from 'C:\Users\jebene\git\Jacquard\jacquard\translate.pyc'>",Cwd="C:\Users\jebene\git">
+##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">
 ##priorSomaticIndelRate=1e-06
 ##reference=file:ucsc.hg19.fasta
 ##source=strelka

test/functional_tests/01_translate/benchmark/tiny.strelka.snvs.translatedTags.vcf

@@ -3,7 +3,7 @@
 ##fileDate=20140709
 ##germlineSnvTheta=0.001
 ##jacquard.translate.caller=Strelka
-##jacquard=<Timestamp="2015-03-30 13:30:01",Command="<module 'jacquard.translate' from 'C:\Users\jebene\git\Jacquard\jacquard\translate.pyc'>",Cwd="C:\Users\jebene\git">
+##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">
 ##priorSomaticSnvRate=1e-06
 ##reference=file:ucsc.hg19.fasta
 ##source=strelka

test/functional_tests/01_translate/benchmark/tiny.varscan.indel.translatedTags.vcf

@@ -1,6 +1,6 @@
 ##fileformat=VCFv4.1
 ##jacquard.translate.caller=VarScan
-##jacquard=<Timestamp="2015-03-30 13:30:01",Command="<module 'jacquard.translate' from 'C:\Users\jebene\git\Jacquard\jacquard\translate.pyc'>",Cwd="C:\Users\jebene\git">
+##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">
 ##source=VarScan2
 ##FILTER=<ID=JQ_EXCLUDE_MALFORMED_ALT,Description="The the format of the alternate allele value for this variant record does not comply with VCF standard.">
 ##FILTER=<ID=JQ_EXCLUDE_MALFORMED_REF,Description="The format of the reference value for this variant record does not comply with VCF standard.">
@@ -24,28 +24,29 @@
 ##FORMAT=<ID=JQ_VS_CALLER_PASSED,Number=1,Type=Integer,Description="1 = variant FILTER is PASS in original VCF">
 ##FORMAT=<ID=JQ_VS_CALLER_REPORTED,Number=1,Type=Integer,Description="1 = variant present in original VCF">
 ##FORMAT=<ID=JQ_VS_DP,Number=1,Type=Float,Description="Jacquard depth for VarScan (based on DP)">
+##FORMAT=<ID=JQ_VS_GT,Number=1,Type=String,Description="Jacquard genotype (based on GT)">
 ##FORMAT=<ID=JQ_VS_HC_SOM,Number=1,Type=Integer,Description="Jacquard somatic status for VarScan: 0=non-somatic,1=somatic (based on SOMATIC info tag and if sample is TUMOR)">
 ##FORMAT=<ID=RD,Number=1,Type=Integer,Description="Depth of reference-supporting bases (reads1)">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NORMAL	TUMOR
-chr1	15903	.	G	GC	.	JQ_VS_LOW_CONFIDENCE	DP=21;SS=1;SSC=0;GPV=1.8578E-12;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4:JQ_VS_CALLER_REPORTED:JQ_VS_CALLER_PASSED:JQ_VS_AF:JQ_VS_DP:JQ_VS_HC_SOM	1/1:.:11:0:11:100%:0,0,10,1:1:0:1.0:11:0	1/1:.:10:0:10:100%:0,0,7,3:1:0:1.0:10:0
-chr1	63735	.	CCTA	C	.	JQ_VS_LOW_CONFIDENCE	DP=72;SS=1;SSC=2;GPV=1.7783E-26;SPV=5.4858E-1	GT:GQ:DP:RD:AD:FREQ:DP4:JQ_VS_CALLER_REPORTED:JQ_VS_CALLER_PASSED:JQ_VS_AF:JQ_VS_DP:JQ_VS_HC_SOM	1/1:.:37:8:29:78.38%:3,5,6,23:1:0:0.78:37:0	1/1:.:35:7:28:80%:1,6,9,19:1:0:0.8:35:0
-chr1	129010	.	AATG	A	.	JQ_VS_LOW_CONFIDENCE	DP=50;SS=1;SSC=6;GPV=1.1557E-4;SPV=2.505E-1	GT:GQ:DP:RD:AD:FREQ:DP4:JQ_VS_CALLER_REPORTED:JQ_VS_CALLER_PASSED:JQ_VS_AF:JQ_VS_DP:JQ_VS_HC_SOM	0/1:.:23:19:4:17.39%:16,3,3,1:1:0:0.17:23:0	0/1:.:27:19:8:29.63%:16,3,6,2:1:0:0.30:27:0
-chr1	267355	.	TATA	T	.	JQ_VS_LOW_CONFIDENCE	DP=124;SS=1;SSC=1;GPV=3.1666E-17;SPV=6.5943E-1	GT:GQ:DP:RD:AD:FREQ:DP4:JQ_VS_CALLER_REPORTED:JQ_VS_CALLER_PASSED:JQ_VS_AF:JQ_VS_DP:JQ_VS_HC_SOM	0/1:.:46:28:18:39.13%:4,24,1,17:1:0:0.39:46:0	0/1:.:78:49:29:37.18%:5,44,3,26:1:0:0.37:78:0
-chr1	668394	.	AG	A	.	JQ_VS_LOW_CONFIDENCE	DP=43;SS=1;SSC=4;GPV=1.3525E-7;SPV=3.895E-1	GT:GQ:DP:RD:AD:FREQ:DP4:JQ_VS_CALLER_REPORTED:JQ_VS_CALLER_PASSED:JQ_VS_AF:JQ_VS_DP:JQ_VS_HC_SOM	0/1:.:23:13:9:40.91%:11,2,7,2:1:0:0.41:23:0	0/1:.:20:10:10:50%:9,1,9,1:1:0:0.5:20:0
-chr1	721104	.	TA	T	.	JQ_VS_LOW_CONFIDENCE	DP=20;SOMATIC;SS=2;SSC=11;GPV=1E0;SPV=6.8111E-2	GT:GQ:DP:RD:AD:FREQ:DP4:JQ_VS_CALLER_REPORTED:JQ_VS_CALLER_PASSED:JQ_VS_AF:JQ_VS_DP:JQ_VS_HC_SOM	1/1:.:9:9:0:0%:9,0,0,0:1:0:0.0:9:0	0/1:.:11:7:4:36.36%:7,0,4,0:1:0:0.36:11:0
-chr1	761957	.	A	AT	.	JQ_VS_LOW_CONFIDENCE	DP=49;SS=1;SSC=7;GPV=8.6743E-25;SPV=1.7781E-1	GT:GQ:DP:RD:AD:FREQ:DP4:JQ_VS_CALLER_REPORTED:JQ_VS_CALLER_PASSED:JQ_VS_AF:JQ_VS_DP:JQ_VS_HC_SOM	1/1:.:21:0:21:100%:0,0,21,0:1:0:1.0:21:0	1/1:.:28:3:25:89.29%:3,0,25,0:1:0:0.89:28:0
-chr1	866511	.	C	CCCCT	.	JQ_VS_LOW_CONFIDENCE	DP=54;SS=1;SSC=0;GPV=5.3813E-5;SPV=9.8141E-1	GT:GQ:DP:RD:AD:FREQ:DP4:JQ_VS_CALLER_REPORTED:JQ_VS_CALLER_PASSED:JQ_VS_AF:JQ_VS_DP:JQ_VS_HC_SOM	0/1:.:26:17:9:34.62%:1,16,3,6:1:0:0.35:26:0	0/1:.:28:24:4:14.29%:5,19,1,3:1:0:0.14:28:0
-chr1	874950	.	T	TCCCTGGAGGACC	.	JQ_VS_LOW_CONFIDENCE	DP=28;SS=1;SSC=0;GPV=4.6796E-5;SPV=9.7397E-1	GT:GQ:DP:RD:AD:FREQ:DP4:JQ_VS_CALLER_REPORTED:JQ_VS_CALLER_PASSED:JQ_VS_AF:JQ_VS_DP:JQ_VS_HC_SOM	0/1:.:11:4:7:63.64%:0,4,0,7:1:0:0.64:11:0	0/1:.:17:10:5:33.33%:1,9,0,5:1:0:0.33:17:0
-chr1	880639	.	TC	T	.	JQ_VS_LOW_CONFIDENCE	DP=32;SS=1;SSC=0;GPV=5.4567E-19;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4:JQ_VS_CALLER_REPORTED:JQ_VS_CALLER_PASSED:JQ_VS_AF:JQ_VS_DP:JQ_VS_HC_SOM	1/1:.:13:0:13:100%:0,0,4,9:1:0:1.0:13:0	1/1:.:19:0:19:100%:0,0,5,14:1:0:1.0:19:0
-chr1	894535	.	G	GC	.	JQ_VS_LOW_CONFIDENCE	DP=25;SOMATIC;SS=2;SSC=9;GPV=1E0;SPV=1.2435E-1	GT:GQ:DP:RD:AD:FREQ:DP4:JQ_VS_CALLER_REPORTED:JQ_VS_CALLER_PASSED:JQ_VS_AF:JQ_VS_DP:JQ_VS_HC_SOM	0/0:.:12:12:0:0%:3,9,0,0:1:0:0.0:12:0	0/1:.:13:10:3:23.08%:0,10,1,2:1:0:0.23:13:0
-chr1	948846	.	T	TA	.	JQ_VS_LOW_CONFIDENCE	DP=25;SS=1;SSC=0;GPV=7.9107E-15;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4:JQ_VS_CALLER_REPORTED:JQ_VS_CALLER_PASSED:JQ_VS_AF:JQ_VS_DP:JQ_VS_HC_SOM	1/1:.:11:0:11:100%:0,0,11,0:1:0:1.0:11:0	1/1:.:14:0:14:100%:0,0,12,2:1:0:1.0:14:0
-chr1	978603	.	CCT	C	.	JQ_VS_LOW_CONFIDENCE	DP=53;SS=1;SSC=9;GPV=7.091E-10;SPV=1.1409E-1	GT:GQ:DP:RD:AD:FREQ:DP4:JQ_VS_CALLER_REPORTED:JQ_VS_CALLER_PASSED:JQ_VS_AF:JQ_VS_DP:JQ_VS_HC_SOM	0/1:.:29:18:11:37.93%:11,7,10,1:1:0:0.38:29:0	0/1:.:24:10:14:58.33%:7,3,11,3:1:0:0.58:24:0
-chr1	985443	.	AG	A	.	JQ_VS_LOW_CONFIDENCE	DP=25;SOMATIC;SS=2;SSC=16;GPV=1E0;SPV=2.2311E-2	GT:GQ:DP:RD:AD:FREQ:DP4:JQ_VS_CALLER_REPORTED:JQ_VS_CALLER_PASSED:JQ_VS_AF:JQ_VS_DP:JQ_VS_HC_SOM	0/0:.:10:10:0:0%:9,1,0,0:1:0:0.0:10:0	0/1:.:15:8:6:42.86%:8,0,5,1:1:0:0.43:15:0
-chr1	1116222	.	CG	C	.	JQ_VS_LOW_CONFIDENCE	DP=22;SOMATIC;SS=2;SSC=9;GPV=1E0;SPV=1.0714E-1	GT:GQ:DP:RD:AD:FREQ:DP4:JQ_VS_CALLER_REPORTED:JQ_VS_CALLER_PASSED:JQ_VS_AF:JQ_VS_DP:JQ_VS_HC_SOM	0/0:.:11:11:0:0%:0,11,0,0:1:0:0.0:11:0	0/1:.:11:8:3:27.27%:0,8,1,2:1:0:0.27:11:0
-chr1	1158441	.	GCA	G	.	JQ_VS_LOW_CONFIDENCE	DP=21;SS=1;SSC=0;GPV=6.592E-4;SPV=8.3437E-1	GT:GQ:DP:RD:AD:FREQ:DP4:JQ_VS_CALLER_REPORTED:JQ_VS_CALLER_PASSED:JQ_VS_AF:JQ_VS_DP:JQ_VS_HC_SOM	0/1:.:8:4:4:50%:4,0,4,0:1:0:0.5:8:0	0/1:.:13:8:5:38.46%:7,1,4,1:1:0:0.38:13:0
-chr1	1215848	.	TA	T	.	JQ_VS_LOW_CONFIDENCE	DP=31;SS=1;SSC=4;GPV=1.0968E-2;SPV=3.9692E-1	GT:GQ:DP:RD:AD:FREQ:DP4:JQ_VS_CALLER_REPORTED:JQ_VS_CALLER_PASSED:JQ_VS_AF:JQ_VS_DP:JQ_VS_HC_SOM	0/1:.:17:12:3:20%:12,0,3,0:1:0:0.2:17:0	0/1:.:14:6:3:33.33%:6,0,2,1:1:0:0.33:14:0
-chr1	1276973	.	G	GACAC	.	JQ_VS_LOW_CONFIDENCE	DP=66;SS=1;SSC=12;GPV=4.14E-31;SPV=5.3588E-2	GT:GQ:DP:RD:AD:FREQ:DP4:JQ_VS_CALLER_REPORTED:JQ_VS_CALLER_PASSED:JQ_VS_AF:JQ_VS_DP:JQ_VS_HC_SOM	1/1:.:29:5:24:82.76%:4,1,17,7:1:0:0.83:29:0	1/1:.:37:1:36:97.3%:1,0,19,17:1:0:0.97:37:0
-chr1	1289367	.	CTG	C	.	JQ_VS_LOW_CONFIDENCE	DP=40;SS=1;SSC=1;GPV=1.1479E-19;SPV=7.3684E-1	GT:GQ:DP:RD:AD:FREQ:DP4:JQ_VS_CALLER_REPORTED:JQ_VS_CALLER_PASSED:JQ_VS_AF:JQ_VS_DP:JQ_VS_HC_SOM	1/1:.:14:1:13:92.86%:0,1,5,8:1:0:0.93:14:0	1/1:.:26:2:24:92.31%:2,0,5,19:1:0:0.92:26:0
-chr1	1333831	.	GA	G	.	JQ_VS_LOW_CONFIDENCE	DP=68;SOMATIC;SS=2;SSC=32;GPV=1E0;SPV=5.6171E-4	GT:GQ:DP:RD:AD:FREQ:DP4:JQ_VS_CALLER_REPORTED:JQ_VS_CALLER_PASSED:JQ_VS_AF:JQ_VS_DP:JQ_VS_HC_SOM	0/0:.:27:27:0:0%:6,21,0,0:1:0:0.0:27:0	0/1:.:41:28:13:31.71%:5,23,5,8:1:0:0.32:41:0
-chr1	1454460	.	G	GC	.	JQ_VS_LOW_CONFIDENCE	DP=32;SOMATIC;SS=2;SSC=8;GPV=1E0;SPV=1.3473E-1	GT:GQ:DP:RD:AD:FREQ:DP4:JQ_VS_CALLER_REPORTED:JQ_VS_CALLER_PASSED:JQ_VS_AF:JQ_VS_DP:JQ_VS_HC_SOM	0/0:.:12:12:0:0%:0,12,0,0:1:0:0.0:12:0	0/1:.:20:16:4:20%:0,16,0,4:1:0:0.2:20:0
-chr1	1479105	.	C	CCT	.	JQ_VS_LOW_CONFIDENCE	DP=31;SS=1;SSC=2;GPV=2.4825E-5;SPV=5.5217E-1	GT:GQ:DP:RD:AD:FREQ:DP4:JQ_VS_CALLER_REPORTED:JQ_VS_CALLER_PASSED:JQ_VS_AF:JQ_VS_DP:JQ_VS_HC_SOM	0/1:.:8:5:3:37.5%:4,1,3,0:1:0:0.38:8:0	0/1:.:23:13:10:43.48%:10,3,7,3:1:0:0.43:23:0
+chr1	15903	.	G	GC	.	JQ_VS_LOW_CONFIDENCE	DP=21;SS=1;SSC=0;GPV=1.8578E-12;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4:JQ_VS_CALLER_REPORTED:JQ_VS_CALLER_PASSED:JQ_VS_AF:JQ_VS_DP:JQ_VS_HC_SOM:JQ_VS_GT	1/1:.:11:0:11:100%:0,0,10,1:1:0:1.0:11:0:1/1	1/1:.:10:0:10:100%:0,0,7,3:1:0:1.0:10:0:1/1
+chr1	63735	.	CCTA	C	.	JQ_VS_LOW_CONFIDENCE	DP=72;SS=1;SSC=2;GPV=1.7783E-26;SPV=5.4858E-1	GT:GQ:DP:RD:AD:FREQ:DP4:JQ_VS_CALLER_REPORTED:JQ_VS_CALLER_PASSED:JQ_VS_AF:JQ_VS_DP:JQ_VS_HC_SOM:JQ_VS_GT	1/1:.:37:8:29:78.38%:3,5,6,23:1:0:0.78:37:0:1/1	1/1:.:35:7:28:80%:1,6,9,19:1:0:0.8:35:0:1/1
+chr1	129010	.	AATG	A	.	JQ_VS_LOW_CONFIDENCE	DP=50;SS=1;SSC=6;GPV=1.1557E-4;SPV=2.505E-1	GT:GQ:DP:RD:AD:FREQ:DP4:JQ_VS_CALLER_REPORTED:JQ_VS_CALLER_PASSED:JQ_VS_AF:JQ_VS_DP:JQ_VS_HC_SOM:JQ_VS_GT	0/1:.:23:19:4:17.39%:16,3,3,1:1:0:0.17:23:0:0/1	0/1:.:27:19:8:29.63%:16,3,6,2:1:0:0.30:27:0:0/1
+chr1	267355	.	TATA	T	.	JQ_VS_LOW_CONFIDENCE	DP=124;SS=1;SSC=1;GPV=3.1666E-17;SPV=6.5943E-1	GT:GQ:DP:RD:AD:FREQ:DP4:JQ_VS_CALLER_REPORTED:JQ_VS_CALLER_PASSED:JQ_VS_AF:JQ_VS_DP:JQ_VS_HC_SOM:JQ_VS_GT	0/1:.:46:28:18:39.13%:4,24,1,17:1:0:0.39:46:0:0/1	0/1:.:78:49:29:37.18%:5,44,3,26:1:0:0.37:78:0:0/1
+chr1	668394	.	AG	A	.	JQ_VS_LOW_CONFIDENCE	DP=43;SS=1;SSC=4;GPV=1.3525E-7;SPV=3.895E-1	GT:GQ:DP:RD:AD:FREQ:DP4:JQ_VS_CALLER_REPORTED:JQ_VS_CALLER_PASSED:JQ_VS_AF:JQ_VS_DP:JQ_VS_HC_SOM:JQ_VS_GT	0/1:.:23:13:9:40.91%:11,2,7,2:1:0:0.41:23:0:0/1	0/1:.:20:10:10:50%:9,1,9,1:1:0:0.5:20:0:0/1
+chr1	721104	.	TA	T	.	JQ_VS_LOW_CONFIDENCE	DP=20;SOMATIC;SS=2;SSC=11;GPV=1E0;SPV=6.8111E-2	GT:GQ:DP:RD:AD:FREQ:DP4:JQ_VS_CALLER_REPORTED:JQ_VS_CALLER_PASSED:JQ_VS_AF:JQ_VS_DP:JQ_VS_HC_SOM:JQ_VS_GT	1/1:.:9:9:0:0%:9,0,0,0:1:0:0.0:9:0:1/1	0/1:.:11:7:4:36.36%:7,0,4,0:1:0:0.36:11:0:0/1
+chr1	761957	.	A	AT	.	JQ_VS_LOW_CONFIDENCE	DP=49;SS=1;SSC=7;GPV=8.6743E-25;SPV=1.7781E-1	GT:GQ:DP:RD:AD:FREQ:DP4:JQ_VS_CALLER_REPORTED:JQ_VS_CALLER_PASSED:JQ_VS_AF:JQ_VS_DP:JQ_VS_HC_SOM:JQ_VS_GT	1/1:.:21:0:21:100%:0,0,21,0:1:0:1.0:21:0:1/1	1/1:.:28:3:25:89.29%:3,0,25,0:1:0:0.89:28:0:1/1
+chr1	866511	.	C	CCCCT	.	JQ_VS_LOW_CONFIDENCE	DP=54;SS=1;SSC=0;GPV=5.3813E-5;SPV=9.8141E-1	GT:GQ:DP:RD:AD:FREQ:DP4:JQ_VS_CALLER_REPORTED:JQ_VS_CALLER_PASSED:JQ_VS_AF:JQ_VS_DP:JQ_VS_HC_SOM:JQ_VS_GT	0/1:.:26:17:9:34.62%:1,16,3,6:1:0:0.35:26:0:0/1	0/1:.:28:24:4:14.29%:5,19,1,3:1:0:0.14:28:0:0/1
+chr1	874950	.	T	TCCCTGGAGGACC	.	JQ_VS_LOW_CONFIDENCE	DP=28;SS=1;SSC=0;GPV=4.6796E-5;SPV=9.7397E-1	GT:GQ:DP:RD:AD:FREQ:DP4:JQ_VS_CALLER_REPORTED:JQ_VS_CALLER_PASSED:JQ_VS_AF:JQ_VS_DP:JQ_VS_HC_SOM:JQ_VS_GT	0/1:.:11:4:7:63.64%:0,4,0,7:1:0:0.64:11:0:0/1	0/1:.:17:10:5:33.33%:1,9,0,5:1:0:0.33:17:0:0/1
+chr1	880639	.	TC	T	.	JQ_VS_LOW_CONFIDENCE	DP=32;SS=1;SSC=0;GPV=5.4567E-19;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4:JQ_VS_CALLER_REPORTED:JQ_VS_CALLER_PASSED:JQ_VS_AF:JQ_VS_DP:JQ_VS_HC_SOM:JQ_VS_GT	1/1:.:13:0:13:100%:0,0,4,9:1:0:1.0:13:0:1/1	1/1:.:19:0:19:100%:0,0,5,14:1:0:1.0:19:0:1/1
+chr1	894535	.	G	GC	.	JQ_VS_LOW_CONFIDENCE	DP=25;SOMATIC;SS=2;SSC=9;GPV=1E0;SPV=1.2435E-1	GT:GQ:DP:RD:AD:FREQ:DP4:JQ_VS_CALLER_REPORTED:JQ_VS_CALLER_PASSED:JQ_VS_AF:JQ_VS_DP:JQ_VS_HC_SOM:JQ_VS_GT	0/0:.:12:12:0:0%:3,9,0,0:1:0:0.0:12:0:0/0	0/1:.:13:10:3:23.08%:0,10,1,2:1:0:0.23:13:0:0/1
+chr1	948846	.	T	TA	.	JQ_VS_LOW_CONFIDENCE	DP=25;SS=1;SSC=0;GPV=7.9107E-15;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4:JQ_VS_CALLER_REPORTED:JQ_VS_CALLER_PASSED:JQ_VS_AF:JQ_VS_DP:JQ_VS_HC_SOM:JQ_VS_GT	1/1:.:11:0:11:100%:0,0,11,0:1:0:1.0:11:0:1/1	1/1:.:14:0:14:100%:0,0,12,2:1:0:1.0:14:0:1/1
+chr1	978603	.	CCT	C	.	JQ_VS_LOW_CONFIDENCE	DP=53;SS=1;SSC=9;GPV=7.091E-10;SPV=1.1409E-1	GT:GQ:DP:RD:AD:FREQ:DP4:JQ_VS_CALLER_REPORTED:JQ_VS_CALLER_PASSED:JQ_VS_AF:JQ_VS_DP:JQ_VS_HC_SOM:JQ_VS_GT	0/1:.:29:18:11:37.93%:11,7,10,1:1:0:0.38:29:0:0/1	0/1:.:24:10:14:58.33%:7,3,11,3:1:0:0.58:24:0:0/1
+chr1	985443	.	AG	A	.	JQ_VS_LOW_CONFIDENCE	DP=25;SOMATIC;SS=2;SSC=16;GPV=1E0;SPV=2.2311E-2	GT:GQ:DP:RD:AD:FREQ:DP4:JQ_VS_CALLER_REPORTED:JQ_VS_CALLER_PASSED:JQ_VS_AF:JQ_VS_DP:JQ_VS_HC_SOM:JQ_VS_GT	0/0:.:10:10:0:0%:9,1,0,0:1:0:0.0:10:0:0/0	0/1:.:15:8:6:42.86%:8,0,5,1:1:0:0.43:15:0:0/1
+chr1	1116222	.	CG	C	.	JQ_VS_LOW_CONFIDENCE	DP=22;SOMATIC;SS=2;SSC=9;GPV=1E0;SPV=1.0714E-1	GT:GQ:DP:RD:AD:FREQ:DP4:JQ_VS_CALLER_REPORTED:JQ_VS_CALLER_PASSED:JQ_VS_AF:JQ_VS_DP:JQ_VS_HC_SOM:JQ_VS_GT	0/0:.:11:11:0:0%:0,11,0,0:1:0:0.0:11:0:0/0	0/1:.:11:8:3:27.27%:0,8,1,2:1:0:0.27:11:0:0/1
+chr1	1158441	.	GCA	G	.	JQ_VS_LOW_CONFIDENCE	DP=21;SS=1;SSC=0;GPV=6.592E-4;SPV=8.3437E-1	GT:GQ:DP:RD:AD:FREQ:DP4:JQ_VS_CALLER_REPORTED:JQ_VS_CALLER_PASSED:JQ_VS_AF:JQ_VS_DP:JQ_VS_HC_SOM:JQ_VS_GT	0/1:.:8:4:4:50%:4,0,4,0:1:0:0.5:8:0:0/1	0/1:.:13:8:5:38.46%:7,1,4,1:1:0:0.38:13:0:0/1
+chr1	1215848	.	TA	T	.	JQ_VS_LOW_CONFIDENCE	DP=31;SS=1;SSC=4;GPV=1.0968E-2;SPV=3.9692E-1	GT:GQ:DP:RD:AD:FREQ:DP4:JQ_VS_CALLER_REPORTED:JQ_VS_CALLER_PASSED:JQ_VS_AF:JQ_VS_DP:JQ_VS_HC_SOM:JQ_VS_GT	0/1:.:17:12:3:20%:12,0,3,0:1:0:0.2:17:0:0/1	0/1:.:14:6:3:33.33%:6,0,2,1:1:0:0.33:14:0:0/1
+chr1	1276973	.	G	GACAC	.	JQ_VS_LOW_CONFIDENCE	DP=66;SS=1;SSC=12;GPV=4.14E-31;SPV=5.3588E-2	GT:GQ:DP:RD:AD:FREQ:DP4:JQ_VS_CALLER_REPORTED:JQ_VS_CALLER_PASSED:JQ_VS_AF:JQ_VS_DP:JQ_VS_HC_SOM:JQ_VS_GT	1/1:.:29:5:24:82.76%:4,1,17,7:1:0:0.83:29:0:1/1	1/1:.:37:1:36:97.3%:1,0,19,17:1:0:0.97:37:0:1/1
+chr1	1289367	.	CTG	C	.	JQ_VS_LOW_CONFIDENCE	DP=40;SS=1;SSC=1;GPV=1.1479E-19;SPV=7.3684E-1	GT:GQ:DP:RD:AD:FREQ:DP4:JQ_VS_CALLER_REPORTED:JQ_VS_CALLER_PASSED:JQ_VS_AF:JQ_VS_DP:JQ_VS_HC_SOM:JQ_VS_GT	1/1:.:14:1:13:92.86%:0,1,5,8:1:0:0.93:14:0:1/1	1/1:.:26:2:24:92.31%:2,0,5,19:1:0:0.92:26:0:1/1
+chr1	1333831	.	GA	G	.	JQ_VS_LOW_CONFIDENCE	DP=68;SOMATIC;SS=2;SSC=32;GPV=1E0;SPV=5.6171E-4	GT:GQ:DP:RD:AD:FREQ:DP4:JQ_VS_CALLER_REPORTED:JQ_VS_CALLER_PASSED:JQ_VS_AF:JQ_VS_DP:JQ_VS_HC_SOM:JQ_VS_GT	0/0:.:27:27:0:0%:6,21,0,0:1:0:0.0:27:0:0/0	0/1:.:41:28:13:31.71%:5,23,5,8:1:0:0.32:41:0:0/1
+chr1	1454460	.	G	GC	.	JQ_VS_LOW_CONFIDENCE	DP=32;SOMATIC;SS=2;SSC=8;GPV=1E0;SPV=1.3473E-1	GT:GQ:DP:RD:AD:FREQ:DP4:JQ_VS_CALLER_REPORTED:JQ_VS_CALLER_PASSED:JQ_VS_AF:JQ_VS_DP:JQ_VS_HC_SOM:JQ_VS_GT	0/0:.:12:12:0:0%:0,12,0,0:1:0:0.0:12:0:0/0	0/1:.:20:16:4:20%:0,16,0,4:1:0:0.2:20:0:0/1
+chr1	1479105	.	C	CCT	.	JQ_VS_LOW_CONFIDENCE	DP=31;SS=1;SSC=2;GPV=2.4825E-5;SPV=5.5217E-1	GT:GQ:DP:RD:AD:FREQ:DP4:JQ_VS_CALLER_REPORTED:JQ_VS_CALLER_PASSED:JQ_VS_AF:JQ_VS_DP:JQ_VS_HC_SOM:JQ_VS_GT	0/1:.:8:5:3:37.5%:4,1,3,0:1:0:0.38:8:0:0/1	0/1:.:23:13:10:43.48%:10,3,7,3:1:0:0.43:23:0:0/1