-
Notifications
You must be signed in to change notification settings - Fork 1
/
Copy pathparsed.example.short.vcf
306 lines (306 loc) · 44.4 KB
/
parsed.example.short.vcf
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
##fileformat=VCFv4.2
##FILTER=<ID=DETP20,Description="Average distance of the variant base to the effective 3' end is less than 0.2">
##FILTER=<ID=DPFilter,Description="DP < 10.0">
##FILTER=<ID=IRC,Description="Unable to grab any sort of readcount for either the reference or the variant allele">
##FILTER=<ID=LowQual,Description="Low quality">
##FILTER=<ID=MMQS100,Description="The average mismatch quality sum of reads supporting the variant is greater than 100">
##FILTER=<ID=MMQSD50,Description="Difference in average mismatch quality sum between variant and reference supporting reads is greater than 50">
##FILTER=<ID=MQD30,Description="Difference in average mapping quality sum between variant and reference supporting reads is greater than 30">
##FILTER=<ID=MVC4,Description="Less than 4 high quality reads support the variant">
##FILTER=<ID=MVF5,Description="Variant allele frequency is less than 0.05">
##FILTER=<ID=NRC,Description="Unable to grab readcounts for variant allele">
##FILTER=<ID=PASS,Description="All filters passed">
##FILTER=<ID=PB10,Description="Average position on read less than 0.1 or greater than 0.9 fraction of the read length">
##FILTER=<ID=QDFilter,Description="QD < 2.0">
##FILTER=<ID=QUALFilter,Description="QUAL < 100.0">
##FILTER=<ID=REJECT,Description="Rejected as a confident somatic mutation">
##FILTER=<ID=RLD25,Description="Difference in average clipped read length between variant and reference supporting reads is greater than 25">
##FILTER=<ID=SB1,Description="Reads supporting the variant have less than 0.01 fraction of the reads on one strand, but reference supporting reads are not similarly biased">
##FILTER=<ID=SnpCluster,Description="SNPs found in clusters">
##FILTER=<ID=Tier1,Description="Confident level 1">
##FILTER=<ID=Tier2,Description="Confident level 2">
##FILTER=<ID=Tier3,Description="Confident level 3">
##FILTER=<ID=Tier4,Description="Confident level 4">
##FILTER=<ID=Tier5,Description="Confident level 5">
##FILTER=<ID=blat,Description="The call did not pass the BLAT filter">
##FILTER=<ID=diffref,Description="Position skipped, different references in files">
##FILTER=<ID=dnmnab,Description="DNA Normal minimum ALT bases is less than user-specified cut-off">
##FILTER=<ID=dnmnap,Description="DNA Normal minimum ALT percentage is less than user-specified cut-off">
##FILTER=<ID=dnmnbq,Description="DNA Normal minimum average ALT base quality is less than user-specified cut-off">
##FILTER=<ID=dnmnrb,Description="DNA Normal minimum REF bases is less than user-specified cut-off">
##FILTER=<ID=dnmnrp,Description="DNA Normal minimum REF percentage is less than user-specified cut-off">
##FILTER=<ID=dnmntb,Description="DNA Normal minimum total bases is less than user-specified cut-off">
##FILTER=<ID=dnmxerr,Description="DNA Normal maximum total ALT percentage attributed to error (sequencing, contamination, etc.) is greater than user-specified cut-off">
##FILTER=<ID=dnmxtb,Description="DNA Normal maximum total bases is greater than user-specified cut-off">
##FILTER=<ID=dnsbias,Description="Strand bias, majority of reads supporting ALT are on forward OR reverse strand">
##FILTER=<ID=dtmnab,Description="DNA Tumor minimum ALT bases is less than user-specified cut-off">
##FILTER=<ID=dtmnap,Description="DNA Tumor minimum ALT percentage is less than user-specified cut-off">
##FILTER=<ID=dtmnbq,Description="DNA Tumor minimum average ALT base quality is less than user-specified cut-off">
##FILTER=<ID=dtmnrb,Description="DNA Tumor minimum REF bases is less than user-specified cut-off">
##FILTER=<ID=dtmnrp,Description="DNA Tumor minimum REF percentage is less than user-specified cut-off">
##FILTER=<ID=dtmntb,Description="DNA Tumor minimum total bases is less than user-specified cut-off">
##FILTER=<ID=dtmxerr,Description="DNA Tumor maximum total ALT percentage attributed to error (sequencing, contamination, etc.) is greater than user-specified cut-off">
##FILTER=<ID=dtmxtb,Description="DNA Tumor maximum total bases is greater than user-specified cut-off">
##FILTER=<ID=dtsbias,Description="Strand bias, majority of reads supporting ALT are on forward OR reverse strand">
##FILTER=<ID=mba,Description="Minimum ALT bases is less than user-specified cut-off">
##FILTER=<ID=mbt,Description="Minimum total bases is less than user-specified cut-off">
##FILTER=<ID=multi,Description="There are multiple ALT alleles across all samples at this position">
##FILTER=<ID=noref,Description="Position skipped, reference=N">
##FILTER=<ID=pbias,Description="The call did not pass the positional bias filter">
##FILTER=<ID=perfect5,Description="There were not enough perfect reads for this position.">
##FILTER=<ID=perfectsbias,Description="A strand bias exists on the perfect reads.">
##FILTER=<ID=rnmnab,Description="RNA Normal minimum ALT bases is less than user-specified cut-off">
##FILTER=<ID=rnmnap,Description="RNA Normal minimum ALT percentage is less than user-specified cut-off">
##FILTER=<ID=rnmnbq,Description="RNA Normal minimum average ALT base quality is less than user-specified cut-off">
##FILTER=<ID=rnmntb,Description="RNA Normal minimum total bases is less than user-specified cut-off">
##FILTER=<ID=rnmxerr,Description="RNA Normal maximum total ALT percentage attributed to error (sequencing, contamination, etc.) is greater than user-specified cut-off">
##FILTER=<ID=rnmxtb,Description="RNA Normal maximum total bases is greater than user-specified cut-off">
##FILTER=<ID=rnsbias,Description="Strand bias, majority of reads supporting ALT are on forward OR reverse strand">
##FILTER=<ID=rtmnab,Description="RNA Tumor minimum ALT bases is less than user-specified cut-off">
##FILTER=<ID=rtmnap,Description="RNA Tumor minimum ALT percentage is less than user-specified cut-off">
##FILTER=<ID=rtmnbq,Description="RNA Tumor minimum average ALT base quality is less than user-specified cut-off">
##FILTER=<ID=rtmntb,Description="RNA Tumor minimum total bases is less than user-specified cut-off">
##FILTER=<ID=rtmxerr,Description="RNA Tumor maximum total ALT percentage attributed to error (sequencing, contamination, etc.) is greater than user-specified cut-off">
##FILTER=<ID=rtmxtb,Description="RNA Tumor maximum total bases is greater than user-specified cut-off">
##FILTER=<ID=rtsbias,Description="Strand bias, majority of reads supporting ALT are on forward OR reverse strand">
##FILTER=<ID=str10,Description="Fails VarScan Strand Filter">
##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
##FORMAT=<ID=AF,Number=.,Type=Float,Description="Fraction of reads supporting alleles">
##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description="Average mapping quality for each allele present in the genotype">
##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description="Occurrence count for each base at this site (A,C,G,T)">
##FORMAT=<ID=BQ,Number=.,Type=Integer,Description="Average base quality for reads supporting alleles">
##FORMAT=<ID=CALLER,Number=.,Type=String,Description="Not provided in original VCF header">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
##FORMAT=<ID=DP4,Number=4,Type=Integer,Description="Number of high-quality ref-forward, ref-reverse, alt-forward and alt-reverse bases">
##FORMAT=<ID=FA,Number=A,Type=Float,Description="Allele fraction of the alternate allele with regard to reference">
##FORMAT=<ID=FREQ,Number=1,Type=String,Description="Variant allele frequency">
##FORMAT=<ID=GMQ,Number=1,Type=Integer,Description="Average mapping quality across all reads">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=HP,Number=.,Type=String,Description="Read-backed phasing haplotype identifiers">
##FORMAT=<ID=IGT,Number=1,Type=String,Description="Genotype when called independently (only filled if called in joint prior mode)">
##FORMAT=<ID=INDEL,Number=1,Type=Integer,Description="Number of indels">
##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description="Joint genotype quality (only filled if called in join prior mode)">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
##FORMAT=<ID=PQ,Number=1,Type=Float,Description="Read-backed phasing quality">
##FORMAT=<ID=PS,Number=1,Type=Integer,Description="ID for set of phased genotypes">
##FORMAT=<ID=RD,Number=1,Type=Integer,Description="Depth of reference-supporting bases (reads1)">
##FORMAT=<ID=SB,Number=.,Type=Float,Description="Strand Bias for reads supporting alleles">
##FORMAT=<ID=SS,Number=1,Type=Integer,Description="Variant status relative to non-adjacent Normal,0=wildtype,1=germline,2=somatic,3=LOH,4=post-transcriptional modification,5=unknown">
##FORMAT=<ID=SSC,Number=1,Type=Integer,Description="Somatic Score">
##FORMAT=<ID=START,Number=1,Type=Integer,Description="Number of reads starting at this position">
##FORMAT=<ID=STOP,Number=1,Type=Integer,Description="Number of reads stopping at this position">
##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description="Variant allele quality">
##FORMAT=<ID=VT,Number=1,Type=String,Description="Variant type, SOMATIC or GERMLINE">
##GATKCommandLine.HaplotypeCaller=<ID=HaplotypeCaller,Version=3.5-0-g36282e4,Date="Fri Apr 06 14:43:01 PDT 2018",Epoch=1523050981703,CommandLineOptions="analysis_type=HaplotypeCaller input_file=[/home/exacloud/lustre1/CompBio/data/mc3_variants/Data_Dec2017/SRR4289732/SRR4289731.reheadered.realigned.cleaned.bam] showFullBamList=false read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] disable_read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=../../Summer2017/core_ref_GRCh37d5/genome.fa nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=500 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 static_quantized_quals=null round_down_quantized=false disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false 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 variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 reference_window_stop=0 logging_level=INFO log_to_file=null help=false version=false out=/home/exacloud/lustre1/CompBio/data/immunotherapy/germline_calls/hg19/SRR4289731.germline.raw.vcf likelihoodCalculationEngine=PairHMM heterogeneousKmerSizeResolution=COMBO_MIN dbsnp=(RodBinding name= source=UNBOUND) dontTrimActiveRegions=false maxDiscARExtension=25 maxGGAARExtension=300 paddingAroundIndels=150 paddingAroundSNPs=20 comp=[] annotation=[] excludeAnnotation=[] group=[Standard, StandardHCAnnotation] debug=false useFilteredReadsForAnnotations=false emitRefConfidence=NONE bamOutput=null bamWriterType=CALLED_HAPLOTYPES disableOptimizations=false annotateNDA=false heterozygosity=0.001 indel_heterozygosity=1.25E-4 standard_min_confidence_threshold_for_calling=30.0 standard_min_confidence_threshold_for_emitting=30.0 max_alternate_alleles=6 input_prior=[] sample_ploidy=2 genotyping_mode=DISCOVERY alleles=(RodBinding name= source=UNBOUND) contamination_fraction_to_filter=0.0 contamination_fraction_per_sample_file=null p_nonref_model=null exactcallslog=null output_mode=EMIT_VARIANTS_ONLY allSitePLs=false gcpHMM=10 pair_hmm_implementation=VECTOR_LOGLESS_CACHING pair_hmm_sub_implementation=ENABLE_ALL always_load_vector_logless_PairHMM_lib=false phredScaledGlobalReadMismappingRate=45 noFpga=false sample_name=null kmerSize=[10, 25] dontIncreaseKmerSizesForCycles=false allowNonUniqueKmersInRef=false numPruningSamples=1 recoverDanglingHeads=false doNotRecoverDanglingBranches=false minDanglingBranchLength=4 consensus=false maxNumHaplotypesInPopulation=128 errorCorrectKmers=false minPruning=2 debugGraphTransformations=false allowCyclesInKmerGraphToGeneratePaths=false graphOutput=null kmerLengthForReadErrorCorrection=25 minObservationsForKmerToBeSolid=20 GVCFGQBands=[1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 70, 80, 90, 99] indelSizeToEliminateInRefModel=10 min_base_quality_score=10 includeUmappedReads=false useAllelesTrigger=false doNotRunPhysicalPhasing=true keepRG=null justDetermineActiveRegions=false dontGenotype=false dontUseSoftClippedBases=false captureAssemblyFailureBAM=false errorCorrectReads=false pcr_indel_model=CONSERVATIVE maxReadsInRegionPerSample=10000 minReadsPerAlignmentStart=10 mergeVariantsViaLD=false activityProfileOut=null activeRegionOut=null activeRegionIn=null activeRegionExtension=null forceActive=false activeRegionMaxSize=null bandPassSigma=null maxProbPropagationDistance=50 activeProbabilityThreshold=0.002 min_mapping_quality_score=20 filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
##GATKCommandLine.ReadBackedPhasing=<ID=ReadBackedPhasing,Version=3.5-0-g36282e4,Date="Tue Jan 29 21:44:13 PST 2019",Epoch=1548827053622,CommandLineOptions="analysis_type=ReadBackedPhasing input_file=[/home/exacloud/lustre1/CompBio/data/mc3_variants/Data_Dec2017/SRR4289732/SRR4289732.reheadered.realigned.cleaned.bam] showFullBamList=false read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] disable_read_filter=[] intervals=[/home/exacloud/lustre1/CompBio/projs/RThompson/immunotherapy/jobs/readbackedphasing/vcfs/Hugo_Pt32.SRR4289732.sorted.vcf] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/home/exacloud/lustre1/CompBio/projs/RThompson/immunotherapy/jobs/mc3/reference_data/core_ref_GRCh37d5/genome.fa nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 static_quantized_quals=null round_down_quantized=false disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false 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 variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 reference_window_stop=0 logging_level=INFO log_to_file=null help=false version=false debug=false variant=(RodBinding name=variant source=/home/exacloud/lustre1/CompBio/projs/RThompson/immunotherapy/jobs/readbackedphasing/vcfs/Hugo_Pt32.SRR4289732.sorted.vcf) out=htsjdk.variant.variantcontext.writer.SortingVariantContextWriter cacheWindowSize=20000 maxPhaseSites=10 phaseQualityThresh=20.0 variantStatsFilePrefix=null min_base_quality_score=17 min_mapping_quality_score=20 sampleToPhase=null permitNoSampleOverlap=false enableMergePhasedSegregatingPolymorphismsToMNP=false maxGenomicDistanceForMNP=1 outputMultipleBaseCountsFile=null filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
##GATKCommandLine.VariantFiltration=<ID=VariantFiltration,Version=3.5-0-g36282e4,Date="Fri Apr 06 18:03:03 PDT 2018",Epoch=1523062983562,CommandLineOptions="analysis_type=VariantFiltration input_file=[] showFullBamList=false read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] disable_read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=../../Summer2017/core_ref_GRCh37d5/genome.fa nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 static_quantized_quals=null round_down_quantized=false disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false 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 variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 reference_window_stop=0 logging_level=INFO log_to_file=null help=false version=false variant=(RodBinding name=variant source=/home/exacloud/lustre1/CompBio/data/immunotherapy/germline_calls/hg19//SRR4289731.germline.raw.vcf) mask=(RodBinding name= source=UNBOUND) out=/home/exacloud/lustre1/CompBio/data/immunotherapy/germline_calls/hg19/SRR4289731.germline.filtered.vcf filterExpression=[QD < 2.0, QUAL < 100.0, DP < 10.0] filterName=[QDFilter, QUALFilter, DPFilter] genotypeFilterExpression=[] genotypeFilterName=[] clusterSize=3 clusterWindowSize=15 maskExtension=0 maskName=Mask filterNotInMask=false missingValuesInExpressionsShouldEvaluateAsFailing=true invalidatePreviousFilters=false invertFilterExpression=false invertGenotypeFilterExpression=false setFilteredGtToNocall=false filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
##INFO=<ID=BQ,Number=1,Type=Integer,Description="RMS base quality">
##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
##INFO=<ID=ClippingRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref number of hard clipped bases">
##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP Membership">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?">
##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
##INFO=<ID=ExcessHet,Number=1,Type=Float,Description="Phred-scaled p-value for exact test of excess heterozygosity">
##INFO=<ID=FA,Number=1,Type=Float,Description="Overall fraction of reads supporting ALT">
##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
##INFO=<ID=GPV,Number=1,Type=Float,Description="Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls">
##INFO=<ID=HOMLEN,Number=.,Type=Integer,Description="Length of base pair identical micro-homology at event breakpoints">
##INFO=<ID=HOMSEQ,Number=.,Type=String,Description="Sequence of base pair identical micro-homology at event breakpoints">
##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes">
##INFO=<ID=INDEL,Number=1,Type=Integer,Description="Number of indels for all samples">
##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">
##INFO=<ID=MC,Number=.,Type=String,Description="Modification base changes at this position">
##INFO=<ID=MLEAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed">
##INFO=<ID=MLEAF,Number=A,Type=Float,Description="Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed">
##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">
##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
##INFO=<ID=MT,Number=.,Type=String,Description="Modification types at this position">
##INFO=<ID=MUSE,Number=.,Type=String,Description="Variant called by muse">
##INFO=<ID=MUTECT,Number=.,Type=String,Description="Variant called by mutect">
##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
##INFO=<ID=NTLEN,Number=.,Type=Integer,Description="Number of bases inserted in place of deleted code">
##INFO=<ID=OLD_CLUMPED,Number=1,Type=String,Description="Original chr:pos:ref:alt encoding">
##INFO=<ID=OLD_MULTIALLELIC,Number=1,Type=String,Description="Original chr:pos:ref:alt encoding">
##INFO=<ID=OLD_VARIANT,Number=.,Type=String,Description="Original chr:pos:ref:alt encoding">
##INFO=<ID=ORIGIN,Number=.,Type=String,Description="Where the call originated from, the tumor DNA, RNA, or both">
##INFO=<ID=PF,Number=1,Type=Integer,Description="The number of samples carry the variant">
##INFO=<ID=PINDEL,Number=.,Type=String,Description="Variant called by pindel">
##INFO=<ID=PhasingInconsistent,Number=0,Type=Flag,Description="Are the reads significantly haplotype-inconsistent?">
##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
##INFO=<ID=RADIA,Number=.,Type=String,Description="Variant called by radia">
##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
##INFO=<ID=SB,Number=1,Type=Float,Description="Strand bias">
##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description="Indicates if record is a somatic mutation">
##INFO=<ID=SOMATICSNIPER,Number=.,Type=String,Description="Variant called by somaticsniper">
##INFO=<ID=SOR,Number=1,Type=Float,Description="Symmetric Odds Ratio of 2x2 contingency table to detect strand bias">
##INFO=<ID=SPV,Number=1,Type=Float,Description="Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls">
##INFO=<ID=SS,Number=1,Type=Integer,Description="Variant status relative to non-adjacent Normal,0=wildtype,1=germline,2=somatic,3=LOH,4=post-transcriptional modification,5=unknown">
##INFO=<ID=SSC,Number=1,Type=String,Description="Somatic score in Phred scale (0-255) derived from somatic p-value">
##INFO=<ID=START,Number=1,Type=Integer,Description="Number of reads starting at this position across all samples">
##INFO=<ID=STOP,Number=1,Type=Integer,Description="Number of reads stopping at this position across all samples">
##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles">
##INFO=<ID=TYPEOFSV,Number=1,Type=String,Description="Type of structural variant">
##INFO=<ID=VARSCAN,Number=.,Type=String,Description="Variant called by varscan">
##INFO=<ID=VT,Number=1,Type=String,Description="Variant type, can be SNP, INS or DEL">
##contig=<ID=1,length=249250621>
##contig=<ID=2,length=243199373>
##contig=<ID=3,length=198022430>
##contig=<ID=4,length=191154276>
##contig=<ID=5,length=180915260>
##contig=<ID=6,length=171115067>
##contig=<ID=7,length=159138663>
##contig=<ID=8,length=146364022>
##contig=<ID=9,length=141213431>
##contig=<ID=10,length=135534747>
##contig=<ID=11,length=135006516>
##contig=<ID=12,length=133851895>
##contig=<ID=13,length=115169878>
##contig=<ID=14,length=107349540>
##contig=<ID=15,length=102531392>
##contig=<ID=16,length=90354753>
##contig=<ID=17,length=81195210>
##contig=<ID=18,length=78077248>
##contig=<ID=19,length=59128983>
##contig=<ID=20,length=63025520>
##contig=<ID=21,length=48129895>
##contig=<ID=22,length=51304566>
##contig=<ID=X,length=155270560>
##contig=<ID=Y,length=59373566>
##contig=<ID=MT,length=16569>
##contig=<ID=GL000207.1,length=4262>
##contig=<ID=GL000226.1,length=15008>
##contig=<ID=GL000229.1,length=19913>
##contig=<ID=GL000231.1,length=27386>
##contig=<ID=GL000210.1,length=27682>
##contig=<ID=GL000239.1,length=33824>
##contig=<ID=GL000235.1,length=34474>
##contig=<ID=GL000201.1,length=36148>
##contig=<ID=GL000247.1,length=36422>
##contig=<ID=GL000245.1,length=36651>
##contig=<ID=GL000197.1,length=37175>
##contig=<ID=GL000203.1,length=37498>
##contig=<ID=GL000246.1,length=38154>
##contig=<ID=GL000249.1,length=38502>
##contig=<ID=GL000196.1,length=38914>
##contig=<ID=GL000248.1,length=39786>
##contig=<ID=GL000244.1,length=39929>
##contig=<ID=GL000238.1,length=39939>
##contig=<ID=GL000202.1,length=40103>
##contig=<ID=GL000234.1,length=40531>
##contig=<ID=GL000232.1,length=40652>
##contig=<ID=GL000206.1,length=41001>
##contig=<ID=GL000240.1,length=41933>
##contig=<ID=GL000236.1,length=41934>
##contig=<ID=GL000241.1,length=42152>
##contig=<ID=GL000243.1,length=43341>
##contig=<ID=GL000242.1,length=43523>
##contig=<ID=GL000230.1,length=43691>
##contig=<ID=GL000237.1,length=45867>
##contig=<ID=GL000233.1,length=45941>
##contig=<ID=GL000204.1,length=81310>
##contig=<ID=GL000198.1,length=90085>
##contig=<ID=GL000208.1,length=92689>
##contig=<ID=GL000191.1,length=106433>
##contig=<ID=GL000227.1,length=128374>
##contig=<ID=GL000228.1,length=129120>
##contig=<ID=GL000214.1,length=137718>
##contig=<ID=GL000221.1,length=155397>
##contig=<ID=GL000209.1,length=159169>
##contig=<ID=GL000218.1,length=161147>
##contig=<ID=GL000220.1,length=161802>
##contig=<ID=GL000213.1,length=164239>
##contig=<ID=GL000211.1,length=166566>
##contig=<ID=GL000199.1,length=169874>
##contig=<ID=GL000217.1,length=172149>
##contig=<ID=GL000216.1,length=172294>
##contig=<ID=GL000215.1,length=172545>
##contig=<ID=GL000205.1,length=174588>
##contig=<ID=GL000219.1,length=179198>
##contig=<ID=GL000224.1,length=179693>
##contig=<ID=GL000223.1,length=180455>
##contig=<ID=GL000195.1,length=182896>
##contig=<ID=GL000212.1,length=186858>
##contig=<ID=GL000222.1,length=186861>
##contig=<ID=GL000200.1,length=187035>
##contig=<ID=GL000193.1,length=189789>
##contig=<ID=GL000194.1,length=191469>
##contig=<ID=GL000225.1,length=211173>
##contig=<ID=GL000192.1,length=547496>
##contig=<ID=NC_007605,length=171823>
##contig=<ID=hs37d5,length=35477943>
##fileDate=2019-01-24
##reference=file:///home/exacloud/lustre1/CompBio/projs/RThompson/immunotherapy/jobs/mc3/reference_data/core_ref_GRCh37d5/genome.fa
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SRR4289732
1 13656 . CAG C 249.73 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-2.571;ClippingRankSum=-0.471;DP=21;ExcessHet=3.0103;FS=0;MLEAC=1;MLEAF=0.5;MQ=23.81;MQRankSum=-1.267;QD=11.89;ReadPosRankSum=-0.543;SOR=1.071 GT:AD:DP:GQ:PL:VT 0/1:13,8:21:99:287,0,577:GERMLINE
1 14464 . A T 628.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=1.482;ClippingRankSum=-0.074;DP=144;ExcessHet=3.0103;FS=4.973;MLEAC=1;MLEAF=0.5;MQ=32.21;MQRankSum=1.526;QD=4.37;ReadPosRankSum=0.978;SOR=1.068 GT:AD:DP:GQ:HP:PL:VT 0/1:112,32:144:99:14464-1,14464-2:657,0,3071:GERMLINE
1 14542 . A G 329.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=6.28;ClippingRankSum=1.229;DP=125;ExcessHet=3.0103;FS=13.843;MLEAC=1;MLEAF=0.5;MQ=27.39;MQRankSum=-2.003;QD=2.64;ReadPosRankSum=3.27;SOR=3.307 GT:AD:DP:GQ:HP:PL:PQ:VT 0/1:105,20:125:99:14464-1,14464-2:358,0,2873:694.19:GERMLINE
1 14907 . A G 5324.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=7.612;ClippingRankSum=0.315;DP=545;ExcessHet=3.0103;FS=9.37;MLEAC=1;MLEAF=0.5;MQ=36.2;MQRankSum=0.013;QD=9.77;ReadPosRankSum=-1.249;SOR=1.319 GT:AD:DP:GQ:HP:PL:PQ:VT 0/1:379,166:545:99:14464-1,14464-2:5353,0,15436:124.92:GERMLINE
1 14930 . A G 6348.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-1.187;ClippingRankSum=0.629;DP=629;ExcessHet=3.0103;FS=6.72;MLEAC=1;MLEAF=0.5;MQ=36.81;MQRankSum=-1.173;QD=10.09;ReadPosRankSum=0.674;SOR=1.101 GT:AD:DP:GQ:HP:PL:PQ:VT 0/1:434,195:629:99:14464-1,14464-2:6377,0,17009:17876.93:GERMLINE
1 15211 . T G 1474.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=3.121;ClippingRankSum=2.003;DP=100;ExcessHet=3.0103;FS=2.04;MLEAC=1;MLEAF=0.5;MQ=27.66;MQRankSum=0.559;QD=14.75;ReadPosRankSum=-0.906;SOR=0.46 GT:AD:DP:GQ:HP:PL:PQ:VT 0/1:44,56:100:99:14464-1,14464-2:1503,0,1012:1808.79:GERMLINE
1 15274 . A T 634.77 PASS AC=2;AF=1;AN=2;DP=26;ExcessHet=3.0103;FS=0;MLEAC=2;MLEAF=1;MQ=25.18;QD=27.6;SOR=4.003 GT:AD:DP:GQ:PL:VT 1/1:0,23:23:69:663,69,0:GERMLINE
1 15903 . G GC 561.73 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-1.033;ClippingRankSum=-0.767;DP=24;ExcessHet=3.0103;FS=8.566;MLEAC=1;MLEAF=0.5;MQ=40.48;MQRankSum=-1.9;QD=23.41;ReadPosRankSum=0.033;SOR=2.833 GT:AD:DP:GQ:PL:VT 0/1:6,18:24:99:599,0,139:GERMLINE
1 16378 . T C 100.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=1.828;ClippingRankSum=-0.858;DP=21;ExcessHet=3.0103;FS=7.605;MLEAC=1;MLEAF=0.5;MQ=29.88;MQRankSum=-0.634;QD=4.8;ReadPosRankSum=0.037;SOR=2.584 GT:AD:DP:GQ:HP:PL:VT 0/1:14,7:21:99:16378-1,16378-2:129,0,363:GERMLINE
1 16495 . G C 172.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-1.638;ClippingRankSum=-0.133;DP=40;ExcessHet=3.0103;FS=0;MLEAC=1;MLEAF=0.5;MQ=22.91;MQRankSum=-0.31;PhasingInconsistent;QD=4.32;ReadPosRankSum=-0.369;SOR=0.457 GT:AD:DP:GQ:HP:PL:PQ:VT 0/1:28,12:40:99:16378-2,16378-1:201,0,735:97.27:GERMLINE
1 16571 . G A 164.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-4.602;ClippingRankSum=0.736;DP=34;ExcessHet=3.0103;FS=4.901;MLEAC=1;MLEAF=0.5;MQ=22.22;MQRankSum=-0.773;PhasingInconsistent;QD=4.85;ReadPosRankSum=-1.583;SOR=0.051 GT:AD:DP:GQ:HP:PL:PQ:VT 0/1:23,11:34:99:16378-1,16378-2:193,0,519:357.16:GERMLINE
1 16977 . G A 858.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-12.17;ClippingRankSum=1.461;DP=399;ExcessHet=3.0103;FS=3.202;MLEAC=1;MLEAF=0.5;MQ=23.91;MQRankSum=1.134;QD=2.16;ReadPosRankSum=0.694;SOR=0.948 GT:AD:DP:GQ:HP:PL:VT 0/1:325,73:398:99:16977-1,16977-2:887,0,9403:GERMLINE
1 17746 . A G 1323.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-1.079;ClippingRankSum=-0.366;DP=112;ExcessHet=3.0103;FS=0;MLEAC=1;MLEAF=0.5;MQ=38.93;MQRankSum=-1.132;QD=11.82;ReadPosRankSum=-0.902;SOR=0.425 GT:AD:DP:GQ:HP:PL:VT 0/1:65,47:112:99:17746-1,17746-2:1352,0,2051:GERMLINE
1 19190 . GC G 382.73 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=1.312;ClippingRankSum=0.474;DP=105;ExcessHet=3.0103;FS=9.525;MLEAC=1;MLEAF=0.5;MQ=22.09;MQRankSum=0.855;QD=3.83;ReadPosRankSum=-1.169;SOR=1.893 GT:AD:DP:GQ:PL:VT 0/1:79,21:100:99:420,0,2329:GERMLINE
1 20245 . G A 158.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-3.323;ClippingRankSum=0.259;DP=29;ExcessHet=3.0103;FS=0;MLEAC=1;MLEAF=0.5;MQ=29.39;MQRankSum=0.872;QD=5.47;ReadPosRankSum=-1.579;SOR=0.409 GT:AD:DP:GQ:HP:PL:VT 0/1:20,9:29:99:20245-1,20245-2:187,0,550:GERMLINE
1 20304 . G C 251.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-1.01;ClippingRankSum=-0.241;DP=17;ExcessHet=3.0103;FS=0;MLEAC=1;MLEAF=0.5;MQ=26.3;MQRankSum=0.914;PhasingInconsistent;QD=14.81;ReadPosRankSum=-0.433;SOR=0.446 GT:AD:DP:GQ:HP:PL:PQ:VT 0/1:8,9:17:99:20245-1,20245-2:280,0,216:79.83:GERMLINE
1 20321 . A C 221.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=2.177;ClippingRankSum=-0.627;DP=14;ExcessHet=3.0103;FS=0;MLEAC=1;MLEAF=0.5;MQ=22.87;MQRankSum=1.365;PhasingInconsistent;QD=15.84;ReadPosRankSum=-0.471;SOR=0.283 GT:AD:DP:GQ:HP:PL:PQ:VT 0/1:6,8:14:99:20245-1,20245-2:250,0,172:200.03:GERMLINE
1 20467 . C T 115.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-2.843;ClippingRankSum=1.191;DP=12;ExcessHet=3.0103;FS=0;MLEAC=1;MLEAF=0.5;MQ=32.93;MQRankSum=-1.073;PhasingInconsistent;QD=9.65;ReadPosRankSum=-1.813;SOR=0.693 GT:AD:DP:GQ:HP:PL:PQ:VT 0/1:6,6:12:99:20245-1,20245-2:144,0,191:79.83:GERMLINE
1 57856 . T A 555.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=2.195;ClippingRankSum=0.223;DP=44;ExcessHet=3.0103;FS=0;MLEAC=1;MLEAF=0.5;MQ=35.76;MQRankSum=0.458;QD=12.63;ReadPosRankSum=-0.833;SOR=1.681 GT:AD:DP:GQ:HP:PL:VT 0/1:22,22:44:99:57856-1,57856-2:584,0,557:GERMLINE
1 63735 . CCTA C 2857.73 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-1.98;ClippingRankSum=1.201;DP=205;ExcessHet=3.0103;FS=2.185;MLEAC=1;MLEAF=0.5;MQ=34.34;MQRankSum=0.413;QD=14.66;ReadPosRankSum=1.29;SOR=0.886 GT:AD:DP:GQ:PL:VT 0/1:117,78:195:99:2895,0,5221:GERMLINE
1 69270 . A G 1733.77 PASS AC=2;AF=1;AN=2;BaseQRankSum=-1.335;ClippingRankSum=0.54;DP=61;ExcessHet=3.0103;FS=0;MLEAC=2;MLEAF=1;MQ=26.65;MQRankSum=0.824;QD=28.42;ReadPosRankSum=-0.142;SOR=6.837 GT:AD:DP:GQ:PL:VT 1/1:1,60:61:99:1762,153,0:GERMLINE
1 69511 . A G 4859.77 PASS AC=2;AF=1;AN=2;DP=159;ExcessHet=3.0103;FS=0;MLEAC=2;MLEAF=1;MQ=32.04;QD=30.76;SOR=1.04 GT:AD:DP:GQ:PL:VT 1/1:0,158:158:99:4888,474,0:GERMLINE
1 69761 . A T 1061.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=4.754;ClippingRankSum=-0.162;DP=79;ExcessHet=3.0103;FS=0;MLEAC=1;MLEAF=0.5;MQ=32.17;MQRankSum=-1.28;QD=13.44;ReadPosRankSum=0.937;SOR=0.774 GT:AD:DP:GQ:HP:PL:VT 0/1:38,41:79:99:69761-1,69761-2:1090,0,946:GERMLINE
1 69897 . T C 253.53 PASS AC=2;AF=1;AN=2;BaseQRankSum=0.158;ClippingRankSum=-1.423;DP=11;ExcessHet=3.0103;FS=0;MLEAC=2;MLEAF=1;MQ=27.95;MQRankSum=-0.791;QD=23.05;ReadPosRankSum=-0.474;SOR=0.399 GT:AD:DP:GQ:PL:VT 1/1:1,10:11:3:280,3,0:GERMLINE
1 129285 . G A 1506.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-5.699;ClippingRankSum=-2.068;DP=194;ExcessHet=3.0103;FS=38.142;MLEAC=1;MLEAF=0.5;MQ=25.73;MQRankSum=-4.305;QD=7.81;ReadPosRankSum=0.528;SOR=1.384 GT:AD:DP:GQ:HP:PL:VT 0/1:108,85:193:99:129285-1,129285-2:1535,0,2457:GERMLINE
1 133483 . G T 332.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-2.286;ClippingRankSum=1.016;DP=24;ExcessHet=3.0103;FS=5.131;MLEAC=1;MLEAF=0.5;MQ=25;MQRankSum=-0.381;QD=13.87;ReadPosRankSum=-0.508;SOR=2.303 GT:AD:DP:GQ:HP:PL:VT 0/1:7,17:24:99:133483-1,133483-2:361,0,123:GERMLINE
1 135465 . C T 360.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=3.379;ClippingRankSum=-0.438;DP=47;ExcessHet=3.0103;FS=0;MLEAC=1;MLEAF=0.5;MQ=34.83;MQRankSum=1.268;QD=7.68;ReadPosRankSum=1.426;SOR=0.249 GT:AD:DP:GQ:HP:PL:VT 0/1:31,16:47:99:135465-1,135465-2:389,0,835:GERMLINE
1 136048 . C T 3065.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=2.574;ClippingRankSum=0.108;DP=247;ExcessHet=3.0103;FS=0.472;MLEAC=1;MLEAF=0.5;MQ=22.05;MQRankSum=0.208;QD=12.41;ReadPosRankSum=-0.966;SOR=0.659 GT:AD:DP:GQ:HP:PL:VT 0/1:100,147:247:99:136048-1,136048-2:3094,0,1874:GERMLINE
1 137622 . G A 558.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-3.367;ClippingRankSum=-1.427;DP=78;ExcessHet=3.0103;FS=16.969;MLEAC=1;MLEAF=0.5;MQ=21.61;MQRankSum=-2.362;QD=7.16;ReadPosRankSum=2.118;SOR=0.082 GT:AD:DP:GQ:HP:PL:VT 0/1:46,32:78:99:137622-1,137622-2:587,0,1185:GERMLINE
1 137825 . G A 840.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-2.659;ClippingRankSum=-0.306;DP=55;ExcessHet=3.0103;FS=4.315;MLEAC=1;MLEAF=0.5;MQ=26.14;MQRankSum=-0.788;QD=15.29;ReadPosRankSum=0.862;SOR=1.379 GT:AD:DP:GQ:HP:PL:PQ:VT 0/1:16,39:55:99:137622-1,137622-2:869,0,285:684.16:GERMLINE
1 138156 . G T 118.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=1.194;ClippingRankSum=0.678;DP=23;ExcessHet=3.0103;FS=4.619;MLEAC=1;MLEAF=0.5;MQ=22.31;MQRankSum=-0.032;QD=5.16;ReadPosRankSum=-0.936;SOR=2.179 GT:AD:DP:GQ:HP:PL:PQ:VT 0/1:15,8:23:99:137622-1,137622-2:147,0,320:121.68:GERMLINE
1 231504 . G A 546.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-2.637;ClippingRankSum=-0.76;DP=39;ExcessHet=3.0103;FS=0;MLEAC=1;MLEAF=0.5;MQ=22;MQRankSum=0.343;QD=14.02;ReadPosRankSum=1.475;SOR=0.784 GT:AD:DP:GQ:HP:PL:VT 0/1:13,26:39:99:231504-1,231504-2:575,0,214:GERMLINE
1 234378 . A G 866.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-0.933;ClippingRankSum=-0.359;DP=73;ExcessHet=3.0103;FS=5.56;MLEAC=1;MLEAF=0.5;MQ=38.87;MQRankSum=0.447;QD=11.87;ReadPosRankSum=-2.6;SOR=0.24 GT:AD:DP:GQ:HP:PL:VT 0/1:38,35:73:99:234378-1,234378-2:895,0,1034:GERMLINE
1 234481 . T A 1024.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-1.299;ClippingRankSum=-0.773;DP=62;ExcessHet=3.0103;FS=0;MLEAC=1;MLEAF=0.5;MQ=42.56;MQRankSum=-0.698;PhasingInconsistent;QD=16.8;ReadPosRankSum=1.029;SOR=0.665 GT:AD:DP:GQ:HP:PL:PQ:VT 0/1:22,39:61:99:234378-1,234378-2:1053,0,532:1109.01:GERMLINE
1 234609 . T C 346.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=1.92;ClippingRankSum=-0.89;DP=18;ExcessHet=3.0103;FS=10.086;MLEAC=1;MLEAF=0.5;MQ=34.95;MQRankSum=2.763;QD=19.26;ReadPosRankSum=-0.047;SOR=4.125 GT:AD:DP:GQ:HP:PL:PQ:VT 0/1:6,12:18:99:234378-1,234378-2:375,0,131:543.90:GERMLINE
1 568214 . C T 558.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-1.532;ClippingRankSum=0.217;DP=56;ExcessHet=3.0103;FS=1.044;MLEAC=1;MLEAF=0.5;MQ=51.35;MQRankSum=-1.915;QD=9.98;ReadPosRankSum=-0.683;SOR=0.633 GT:AD:DP:GQ:HP:PL:VT 0/1:33,23:56:99:568214-1,568214-2:587,0,955:GERMLINE
1 662029 . G A 487.77 PASS AC=2;AF=1;AN=2;BaseQRankSum=-1.734;ClippingRankSum=1.261;DP=22;ExcessHet=3.0103;FS=0;MLEAC=2;MLEAF=1;MQ=21.05;MQRankSum=-1.576;QD=22.17;ReadPosRankSum=0;SOR=4.804 GT:AD:DP:GQ:PL:VT 1/1:1,21:22:40:516,40,0:GERMLINE
1 662201 . G A 435.77 PASS AC=2;AF=1;AN=2;BaseQRankSum=1.552;ClippingRankSum=-0.274;DP=19;ExcessHet=3.0103;FS=0;MLEAC=2;MLEAF=1;MQ=21.79;MQRankSum=-0.274;QD=22.94;ReadPosRankSum=1.004;SOR=1.609 GT:AD:DP:GQ:PL:VT 1/1:1,18:19:47:464,47,0:GERMLINE
1 662857 . G A 462.77 PASS AC=2;AF=1;AN=2;DP=16;ExcessHet=3.0103;FS=0;MLEAC=2;MLEAF=1;MQ=29.86;QD=28.92;SOR=0.693 GT:AD:DP:GQ:PL:VT 1/1:0,16:16:48:491,48,0:GERMLINE
1 663097 . G C 2622.77 PASS AC=2;AF=1;AN=2;DP=100;ExcessHet=3.0103;FS=0;MLEAC=2;MLEAF=1;MQ=22.92;QD=26.23;SOR=1.993 GT:AD:DP:GQ:PL:VT 1/1:0,100:100:99:2651,300,0:GERMLINE
1 664271 . C A 152.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-3.154;ClippingRankSum=-0.222;DP=18;ExcessHet=3.0103;FS=0;MLEAC=1;MLEAF=0.5;MQ=20.29;MQRankSum=-1.2;QD=8.49;ReadPosRankSum=0.666;SOR=0.512 GT:AD:DP:GQ:HP:PL:VT 0/1:10,8:18:99:664271-1,664271-2:181,0,196:GERMLINE
1 664468 . G T 274.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-4.009;ClippingRankSum=-1.403;DP=58;ExcessHet=3.0103;FS=5.711;MLEAC=1;MLEAF=0.5;MQ=24.16;MQRankSum=0.966;PhasingInconsistent;QD=4.74;ReadPosRankSum=1.555;SOR=1.493 GT:AD:DP:GQ:HP:PL:PQ:VT 0/1:40,18:58:99:664271-2,664271-1:303,0,879:109.60:GERMLINE
1 671892 . C T 543.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.01;ClippingRankSum=-0.884;DP=51;ExcessHet=3.0103;FS=0;MLEAC=1;MLEAF=0.5;MQ=33.59;MQRankSum=1.056;QD=10.66;ReadPosRankSum=0.599;SOR=0.73 GT:AD:DP:GQ:HP:PL:VT 0/1:29,22:51:99:671892-1,671892-2:572,0,843:GERMLINE
1 672209 . G A 121.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-4.333;ClippingRankSum=-0.843;DP=50;ExcessHet=3.0103;FS=20.692;MLEAC=1;MLEAF=0.5;MQ=37.07;MQRankSum=-2.295;PhasingInconsistent;QD=2.44;ReadPosRankSum=0.796;SOR=0.016 GT:AD:DP:GQ:HP:PL:PQ:VT 0/1:39,11:50:99:671892-2,671892-1:150,0,1187:23.39:GERMLINE
1 709135 . T C 115.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=3.005;ClippingRankSum=-0.177;DP=15;ExcessHet=3.0103;FS=2.187;MLEAC=1;MLEAF=0.5;MQ=32.42;MQRankSum=-0.53;QD=7.72;ReadPosRankSum=0.295;SOR=1.371 GT:AD:DP:GQ:HP:PL:VT 0/1:9,6:15:99:709135-1,709135-2:144,0,235:GERMLINE
1 709297 . T C 125.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=4.048;ClippingRankSum=1.444;DP=25;ExcessHet=3.0103;FS=20.017;MLEAC=1;MLEAF=0.5;MQ=20.25;MQRankSum=1.33;QD=5.03;ReadPosRankSum=1.104;SOR=0.005 GT:AD:DP:GQ:HP:PL:PQ:VT 0/1:16,9:25:99:709135-2,709135-1:154,0,320:104.42:GERMLINE
1 718555 . T C 1957.77 PASS AC=2;AF=1;AN=2;DP=54;ExcessHet=3.0103;FS=0;MLEAC=2;MLEAF=1;MQ=49.13;QD=32.61;SOR=2.876 GT:AD:DP:GQ:PL:VT 1/1:0,54:54:99:1986,162,0:GERMLINE
1 744304 . C T 273.77 PASS AC=2;AF=1;AN=2;DP=10;ExcessHet=3.0103;FS=0;MLEAC=2;MLEAF=1;MQ=25.63;QD=27.38;SOR=4.804 GT:AD:DP:GQ:PL:VT 1/1:0,10:10:30:302,30,0:GERMLINE
1 745370 . TA T 127.73 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-1.604;ClippingRankSum=1.035;DP=57;ExcessHet=3.0103;FS=0;MLEAC=1;MLEAF=0.5;MQ=40.01;MQRankSum=-3.151;QD=2.32;ReadPosRankSum=-2.104;SOR=0.346 GT:AD:DP:GQ:PL:VT 0/1:46,9:55:99:165,0,1555:GERMLINE
1 752721 . A G 3691.77 PASS AC=2;AF=1;AN=2;DP=95;ExcessHet=3.0103;FS=0;MLEAC=2;MLEAF=1;MQ=60;QD=38.51;SOR=6.294 GT:AD:DP:GQ:PL:VT 1/1:0,95:95:99:3720,286,0:GERMLINE
1 752894 . T C 1858.77 PASS AC=2;AF=1;AN=2;DP=56;ExcessHet=3.0103;FS=0;MLEAC=2;MLEAF=1;MQ=39.79;QD=33.19;SOR=8.086 GT:AD:DP:GQ:PL:VT 1/1:0,56:56:99:1887,168,0:GERMLINE
1 753269 . C G 1225.77 PASS AC=2;AF=1;AN=2;DP=36;ExcessHet=3.0103;FS=0;MLEAC=2;MLEAF=1;MQ=32.46;QD=34.05;SOR=7.223 GT:AD:DP:GQ:PL:VT 1/1:0,36:36:99:1254,108,0:GERMLINE
1 753405 . C A 2038.77 PASS AC=2;AF=1;AN=2;DP=66;ExcessHet=3.0103;FS=0;MLEAC=2;MLEAF=1;MQ=35.65;QD=30.89;SOR=1.112 GT:AD:DP:GQ:PL:VT 1/1:0,66:66:99:2067,198,0:GERMLINE
1 753425 . T C 1063.77 PASS AC=2;AF=1;AN=2;DP=32;ExcessHet=3.0103;FS=0;MLEAC=2;MLEAF=1;MQ=36.79;QD=33.24;SOR=0.957 GT:AD:DP:GQ:PL:VT 1/1:0,32:32:96:1092,96,0:GERMLINE
1 753474 . C G 1092.77 PASS AC=2;AF=1;AN=2;DP=32;ExcessHet=3.0103;FS=0;MLEAC=2;MLEAF=1;MQ=43.95;QD=34.15;SOR=2.765 GT:AD:DP:GQ:PL:VT 1/1:0,32:32:96:1121,96,0:GERMLINE
1 761957 . A AT 1532.73 PASS AC=2;AF=1;AN=2;DP=38;ExcessHet=3.0103;FS=0;MLEAC=2;MLEAF=1;MQ=38.34;QD=28.52;SOR=7.328 GT:AD:DP:GQ:PL:VT 1/1:0,38:38:99:1570,117,0:GERMLINE
1 762273 . G A 3213.77 PASS AC=2;AF=1;AN=2;DP=95;ExcessHet=3.0103;FS=0;MLEAC=2;MLEAF=1;MQ=37.23;QD=33.83;SOR=2.135 GT:AD:DP:GQ:PL:VT 1/1:0,95:95:99:3242,286,0:GERMLINE
1 762632 . T A 6657.77 PASS AC=2;AF=1;AN=2;BaseQRankSum=2.184;ClippingRankSum=0.985;DP=201;ExcessHet=3.0103;FS=9.146;MLEAC=2;MLEAF=1;MQ=43.03;MQRankSum=2.878;QD=33.12;ReadPosRankSum=-2.635;SOR=0.04 GT:AD:DP:GQ:PL:VT 1/1:4,197:201:99:6686,478,0:GERMLINE
1 801943 . C T 3561.77 PASS AC=2;AF=1;AN=2;BaseQRankSum=1.697;ClippingRankSum=0.052;DP=100;ExcessHet=3.0103;FS=4.771;MLEAC=2;MLEAF=1;MQ=50.57;MQRankSum=0.822;QD=28.67;ReadPosRankSum=1.487;SOR=1.475 GT:AD:DP:GQ:PL:VT 1/1:1,98:99:99:3590,218,0:GERMLINE
1 801957 . CCTGCACTCACATCCCTGACGTCCTCCCGTGCCCTCACGTGGTCCTCCCT C 1677.73 PASS AC=2;AF=1;AN=2;BaseQRankSum=1.892;ClippingRankSum=0.781;DP=89;ExcessHet=3.0103;FS=0;MLEAC=2;MLEAF=1;MQ=48.91;MQRankSum=-0.066;QD=25.04;ReadPosRankSum=0.728;SOR=1.179 GT:AD:DP:GQ:PL:VT 1/1:4,63:67:38:1715,38,0:GERMLINE
hs37d5 35027814 . T C 178.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=2.637;ClippingRankSum=-0.717;DP=11;ExcessHet=3.0103;FS=0;MLEAC=1;MLEAF=0.5;MQ=56.13;MQRankSum=-1.408;QD=16.25;ReadPosRankSum=1.031;SOR=0.859 GT:AD:DP:GQ:HP:PL:PQ:VT 0/1:5,6:11:99:35027800-1,35027800-2:207,0,138:468.44:GERMLINE
hs37d5 35027829 . C T 202.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-1.733;ClippingRankSum=0.578;DP=16;ExcessHet=3.0103;FS=0;MLEAC=1;MLEAF=0.5;MQ=56.55;MQRankSum=-0.683;QD=12.67;ReadPosRankSum=0.578;SOR=0.18 GT:AD:DP:GQ:HP:PL:PQ:VT 0/1:8,8:16:99:35027800-1,35027800-2:231,0,246:489.97:GERMLINE
hs37d5 35027880 . C T 181.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.405;ClippingRankSum=0.752;DP=15;ExcessHet=3.0103;FS=0;MLEAC=1;MLEAF=0.5;MQ=53.61;MQRankSum=-0.637;QD=12.12;ReadPosRankSum=1.331;SOR=0.551 GT:AD:DP:GQ:HP:PL:PQ:VT 0/1:8,7:15:99:35027800-1,35027800-2:210,0,224:489.97:GERMLINE
hs37d5 35027909 . C G 197.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-2.176;ClippingRankSum=-0.872;DP=15;ExcessHet=3.0103;FS=0;MLEAC=1;MLEAF=0.5;MQ=46.36;MQRankSum=-0.556;QD=13.18;ReadPosRankSum=-0.993;SOR=0.892 GT:AD:DP:GQ:HP:PL:PQ:VT 0/1:7,8:15:99:35027800-1,35027800-2:226,0,233:423.41:GERMLINE
hs37d5 35027982 . G A 126.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-2.637;ClippingRankSum=-1.186;DP=11;ExcessHet=3.0103;FS=0;MLEAC=1;MLEAF=0.5;MQ=38.81;MQRankSum=-1.186;QD=11.52;ReadPosRankSum=0.143;SOR=0.859 GT:AD:DP:GQ:HP:PL:PQ:VT 0/1:5,6:11:99:35027800-1,35027800-2:155,0,166:331.90:GERMLINE
hs37d5 35029456 . A C 241.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.752;ClippingRankSum=0.637;DP=15;ExcessHet=3.0103;FS=0;MLEAC=1;MLEAF=0.5;MQ=32.81;MQRankSum=0.174;QD=16.12;ReadPosRankSum=-0.868;SOR=0.941 GT:AD:DP:GQ:HP:PL:VT 0/1:8,7:15:99:35029456-1,35029456-2:270,0,463:GERMLINE
hs37d5 35029459 . A C 241.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=1.215;ClippingRankSum=0.289;DP=15;ExcessHet=3.0103;FS=0;MLEAC=1;MLEAF=0.5;MQ=32.81;MQRankSum=-0.405;QD=16.12;ReadPosRankSum=-1.562;SOR=0.941 GT:AD:DP:GQ:HP:PL:PQ:VT 0/1:8,7:15:99:35029456-1,35029456-2:270,0,463:372.23:GERMLINE