##fileformat=VCFv4.1
##FILTER=<ID=LowQual,Description="Low quality">
##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
##GATKCommandLine=<ID=UnifiedGenotyper,Version=2.8-1-g932cd3a,Date="Sat Jan 25 10:33:56 CET 2014",Epoch=1390642436187,CommandLineOptions="analysis_type=UnifiedGenotyper input_file=[/data_fedor12/BAM/sander/Liver_clones/BIOPSY17513D/mapping/BIOPSY17513D_dedup_realigned_recalibrated.bam, /data_fedor12/BAM/sander/Liver_clones/clone3/mapping/clone3_dedup_realigned_recalibrated.bam, /data_fedor12/BAM/sander/Liver_clones/clone4/mapping/clone4_dedup_realigned_recalibrated.bam, /data_fedor12/BAM/sander/Liver_clones/clone10/mapping/clone10_dedup_realigned_recalibrated.bam, /data_fedor12/BAM/sander/Liver_clones/subclone33/mapping/subclone33_dedup_realigned_recalibrated.bam, /data_fedor12/BAM/sander/Liver_clones/subclone46/mapping/subclone46_dedup_realigned_recalibrated.bam, /data_fedor12/BAM/sander/Liver_clones/subclone105/mapping/subclone105_dedup_realigned_recalibrated.bam] read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] intervals=[/data_fedor13/sander/variant_calling/Liver_clones/.queue/scatterGather/UnifiedGenotyper_noref-1-sg/temp_001_of_500/scatter.intervals] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/data_fedor13/common_data/references/H_sapiens/GATK_b37_bundle_reference/basespace/human_g1k_v37.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=250 baq=OFF baqGapOpenPenalty=40.0 fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 allow_bqsr_on_reduced_bams_despite_repeated_warnings=false 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 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 logging_level=INFO log_to_file=null help=false version=false genotype_likelihoods_model=SNP pcr_error_rate=1.0E-4 computeSLOD=false annotateNDA=false pair_hmm_implementation=LOGLESS_CACHING min_base_quality_score=17 max_deletion_fraction=0.05 allSitePLs=false min_indel_count_for_genotyping=5 min_indel_fraction_per_sample=0.25 indelGapContinuationPenalty=10 indelGapOpenPenalty=45 indelHaplotypeSize=80 indelDebug=false ignoreSNPAlleles=false allReadsSP=false ignoreLaneInfo=false reference_sample_calls=(RodBinding name= source=UNBOUND) reference_sample_name=null sample_ploidy=2 min_quality_score=1 max_quality_score=40 site_quality_prior=20 min_power_threshold_for_calling=0.95 min_reference_depth=100 exclude_filtered_reference_sites=false output_mode=EMIT_VARIANTS_ONLY heterozygosity=0.001 indel_heterozygosity=1.25E-4 genotyping_mode=DISCOVERY standard_min_confidence_threshold_for_calling=30.0 standard_min_confidence_threshold_for_emitting=30.0 alleles=(RodBinding name= source=UNBOUND) max_alternate_alleles=6 input_prior=[] contamination_fraction_to_filter=0.0 contamination_fraction_per_sample_file=null p_nonref_model=EXACT_INDEPENDENT exactcallslog=null dbsnp=(RodBinding name= source=UNBOUND) comp=[] out=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 onlyEmitSamples=[] debug_file=null metrics_file=null annotation=[] excludeAnnotation=[] 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=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
##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=Dels,Number=1,Type=Float,Description="Fraction of Reads Containing Spanning Deletions">
##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes">
##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=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=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
##INFO=<ID=RPA,Number=.,Type=Integer,Description="Number of times tandem repeat unit is repeated, for each allele (including reference)">
##INFO=<ID=RU,Number=1,Type=String,Description="Tandem repeat unit (bases)">
##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
##INFO=<ID=STR,Number=0,Type=Flag,Description="Variant is a short tandem repeat">
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##reference=file:human_g1k_v37.fasta
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	Original	s1t1	s2t1	s3t1	s1t2	s2t2	s3t2
1	10257	.	A	C	77.69	.	AC=1;AF=0.071;AN=14;BaseQRankSum=-0.066;DP=1518;Dels=0.00;FS=24.214;HaplotypeScore=226.5209;MLEAC=1;MLEAF=0.071;MQ=25.00;MQ0=329;MQRankSum=-1.744;QD=0.37;ReadPosRankSum=1.551	GT:AD:DP:GQ:PL	0/0:151,8:159:99:0,195,2282	0/0:219,22:242:99:0,197,2445	0/0:227,22:249:90:0,90,2339	0/0:226,22:249:99:0,159,2695	0/0:166,18:186:99:0,182,1989	0/1:185,27:212:99:111,0,2387	0/0:201,15:218:24:0,24,1972
1	10291	.	C	T	1031.89	.	AC=7;AF=0.500;AN=14;BaseQRankSum=4.367;DP=1433;Dels=0.00;FS=0.696;HaplotypeScore=101.0885;MLEAC=7;MLEAF=0.500;MQ=26.96;MQ0=225;MQRankSum=0.087;QD=0.72;ReadPosRankSum=-1.640	GT:AD:DP:GQ:PL	0/1:145,16:165:23:23,0,491	0/1:218,26:249:29:29,0,611	0/1:214,30:249:99:145,0,801	0/1:213,32:247:20:20,0,1031	0/1:122,36:161:99:347,0,182	0/1:131,27:163:99:255,0,508	0/1:156,31:189:99:252,0,372
1	10297	.	C	T	187.21	.	AC=5;AF=0.357;AN=14;BaseQRankSum=-2.778;DP=1440;Dels=0.00;FS=0.000;HaplotypeScore=123.6373;MLEAC=5;MLEAF=0.357;MQ=27.26;MQ0=217;MQRankSum=-2.914;QD=0.18;ReadPosRankSum=1.927	GT:AD:DP:GQ:PL	0/1:155,18:182:44:44,0,654	0/1:218,23:246:21:21,0,673	0/1:219,26:250:41:41,0,898	0/0:207,30:246:39:0,39,963	0/0:137,20:165:21:0,21,363	0/1:124,27:158:65:65,0,435	0/1:151,27:183:63:63,0,485
1	10303	.	C	T	166.50	.	AC=3;AF=0.214;AN=14;BaseQRankSum=-3.960;DP=1460;Dels=0.00;FS=2.121;HaplotypeScore=138.0883;MLEAC=2;MLEAF=0.143;MQ=27.29;MQ0=220;MQRankSum=-2.873;QD=0.27;ReadPosRankSum=1.756	GT:AD:DP:GQ:PL	0/1:169,25:198:99:195,0,609	0/1:211,31:247:1:1,0,656	0/0:214,28:248:7:0,7,982	0/0:214,32:248:25:0,25,980	0/0:146,17:172:2:0,2,353	0/1:123,23:157:17:17,0,541	0/0:156,22:182:19:0,19,413
1	10315	.	C	T	108.20	.	AC=3;AF=0.214;AN=14;BaseQRankSum=-3.769;DP=1500;Dels=0.01;FS=1.493;HaplotypeScore=169.3933;MLEAC=3;MLEAF=0.214;MQ=26.95;MQ0=241;MQRankSum=-4.511;QD=0.19;ReadPosRankSum=2.373	GT:AD:DP:GQ:PL	0/1:181,26:212:41:41,0,618	0/0:223,17:246:99:0,102,832	0/0:219,20:242:66:0,66,924	0/0:217,23:245:99:0,109,1384	0/1:155,27:190:97:97,0,328	0/1:130,20:157:10:10,0,531	0/0:163,24:189:5:0,5,450
1	10321	.	C	T	106.30	.	AC=5;AF=0.357;AN=14;BaseQRankSum=3.045;DP=1537;Dels=0.01;FS=5.835;HaplotypeScore=220.1531;MLEAC=5;MLEAF=0.357;MQ=26.69;MQ0=258;MQRankSum=-4.870;QD=0.10;ReadPosRankSum=0.815	GT:AD:DP:GQ:PL	0/1:189,25:218:30:30,0,810	0/0:219,22:246:24:0,24,593	0/1:218,27:248:34:34,0,1134	0/0:220,22:248:56:0,56,1207	0/1:168,23:193:19:19,0,493	0/1:139,22:164:46:46,0,689	0/1:167,26:196:20:20,0,522
1	10327	.	T	C	1215.15	.	AC=7;AF=0.500;AN=14;BaseQRankSum=3.585;DP=1641;Dels=0.02;FS=6.639;HaplotypeScore=237.4339;MLEAC=7;MLEAF=0.500;MQ=25.22;MQ0=321;MQRankSum=4.402;QD=0.74;ReadPosRankSum=3.957	GT:AD:DP:GQ:PL	0/1:178,56:237:99:178,0,848	0/1:178,60:238:99:320,0,575	0/1:185,40:229:99:236,0,679	0/1:184,52:237:99:358,0,544	0/1:165,43:209:57:57,0,726	0/1:151,31:183:9:9,0,780	0/1:164,46:210:96:96,0,550
1	10583	.	G	A	699.85	.	AC=7;AF=0.500;AN=14;BaseQRankSum=-4.714;DP=129;Dels=0.00;FS=7.556;HaplotypeScore=0.6677;MLEAC=7;MLEAF=0.500;MQ=41.33;MQ0=2;MQRankSum=-2.309;QD=5.43;ReadPosRankSum=-0.296	GT:AD:DP:GQ:PL	0/1:5,3:8:58:58,0,133	0/1:12,12:24:99:231,0,287	0/1:16,4:21:38:38,0,491	0/1:19,4:23:57:57,0,494	0/1:9,6:15:99:140,0,180	0/1:11,8:19:99:173,0,235	0/1:15,4:19:42:42,0,344
1	10665	.	C	G	56.61	.	AC=2;AF=0.250;AN=8;BaseQRankSum=2.219;DP=28;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=0.250;MQ=25.41;MQ0=15;MQRankSum=0.185;QD=4.72;ReadPosRankSum=1.849	GT:AD:DP:GQ:PL	./.	./.	0/1:4,3:7:57:57,0,78	0/1:3,2:5:23:30,0,23	./.	0/0:2,0:2:3:0,3,26	0/0:6,1:7:6:0,6,49
1	10694	.	C	G	85.78	.	AC=4;AF=1.00;AN=4;DP=22;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=4;MLEAF=1.00;MQ=17.21;MQ0=17;QD=8.58	GT:AD:DP:GQ:PL	./.	./.	1/1:2,3:5:6:74,6,0	1/1:3,2:5:3:35,3,0	./.	./.	./.
1	10723	.	C	G	73.85	.	AC=4;AF=0.667;AN=6;BaseQRankSum=1.300;DP=18;Dels=0.00;FS=3.680;HaplotypeScore=0.0000;MLEAC=4;MLEAF=0.667;MQ=20.49;MQ0=11;MQRankSum=1.754;QD=8.21;ReadPosRankSum=0.000	GT:AD:DP:GQ:PL	./.	./.	1/1:2,2:4:6:66,6,0	1/1:4,1:5:3:36,3,0	./.	./.	0/0:6,0:6:3:0,3,33
1	12783	.	G	A	4330.85	.	AC=7;AF=0.500;AN=14;BaseQRankSum=12.671;DP=939;Dels=0.00;FS=0.000;HaplotypeScore=1.4998;MLEAC=7;MLEAF=0.500;MQ=14.64;MQ0=602;MQRankSum=-3.992;QD=4.61;ReadPosRankSum=0.195	GT:AD:DP:GQ:PL	0/1:24,34:58:82:174,0,82	0/1:80,84:164:99:658,0,433	0/1:59,85:144:99:670,0,407	0/1:68,114:182:99:1074,0,463	0/1:58,68:126:99:437,0,310	0/1:37,66:103:99:446,0,369	0/1:62,96:158:99:911,0,417
1	13116	.	T	G	2592.85	.	AC=7;AF=0.500;AN=14;BaseQRankSum=-5.563;DP=721;Dels=0.00;FS=381.256;HaplotypeScore=2.5606;MLEAC=7;MLEAF=0.500;MQ=23.97;MQ0=222;MQRankSum=-14.896;QD=3.60;ReadPosRankSum=3.079	GT:AD:DP:GQ:PL	0/1:20,12:32:92:92,0,300	0/1:84,47:131:99:479,0,1548	0/1:65,37:102:99:441,0,1153	0/1:94,57:152:99:584,0,1993	0/1:61,43:104:99:360,0,1199	0/1:54,33:88:99:221,0,986	0/1:62,47:109:99:455,0,1128
1	13118	.	A	G	2317.85	.	AC=7;AF=0.500;AN=14;BaseQRankSum=-9.647;DP=703;Dels=0.00;FS=362.380;HaplotypeScore=2.3393;MLEAC=7;MLEAF=0.500;MQ=23.54;MQ0=228;MQRankSum=-14.592;QD=3.30;ReadPosRankSum=3.437	GT:AD:DP:GQ:PL	0/1:21,13:34:95:95,0,277	0/1:82,47:129:99:444,0,1445	0/1:65,36:101:99:412,0,1179	0/1:92,53:145:99:455,0,1989	0/1:58,40:99:99:312,0,1216	0/1:52,33:85:99:186,0,1000	0/1:61,47:108:99:453,0,1079
1	13178	.	G	A	72.69	.	AC=2;AF=0.143;AN=14;BaseQRankSum=-2.194;DP=929;Dels=0.00;FS=8.154;HaplotypeScore=1.8585;MLEAC=2;MLEAF=0.143;MQ=13.49;MQ0=590;MQRankSum=-3.030;QD=0.38;ReadPosRankSum=-0.383	GT:AD:DP:GQ:PL	0/1:49,3:52:11:11,0,292	0/0:161,11:172:60:0,60,1328	0/1:122,15:137:99:99,0,936	0/0:164,8:172:99:0,112,1436	0/0:120,9:129:62:0,62,771	0/0:113,6:119:12:0,12,885	0/0:138,10:148:99:0,112,1596
1	13302	.	C	T	1067.42	.	AC=6;AF=0.429;AN=14;BaseQRankSum=11.584;DP=692;Dels=0.00;FS=86.736;HaplotypeScore=2.8260;MLEAC=6;MLEAF=0.429;MQ=27.08;MQ0=150;MQRankSum=-14.794;QD=1.63;ReadPosRankSum=-9.193	GT:AD:DP:GQ:PL	0/0:26,10:36:41:0,41,616	0/1:91,45:136:99:183,0,2085	0/1:71,28:99:86:86,0,1557	0/1:96,50:146:99:333,0,2098	0/1:55,34:90:99:283,0,1321	0/1:47,18:65:99:157,0,943	0/1:89,28:117:67:67,0,1921