117 lines
47 KiB
Plaintext
117 lines
47 KiB
Plaintext
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##fileformat=VCFv4.1
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##ALT=<ID=DEL,Description="Deletion">
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##FORMAT=<ID=DS,Number=1,Type=Float,Description="Genotype dosage from MaCH/Thunder">
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##FORMAT=<ID=GL,Number=.,Type=Float,Description="Genotype Likelihoods">
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##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
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##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele, ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/pilot_data/technical/reference/ancestral_alignments/README">
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##INFO=<ID=AC,Number=.,Type=Integer,Description="Alternate Allele Count">
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##INFO=<ID=AF,Number=1,Type=Float,Description="Global Allele Frequency based on AC/AN">
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##INFO=<ID=AFR_AF,Number=1,Type=Float,Description="Allele Frequency for samples from AFR based on AC/AN">
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##INFO=<ID=AMR_AF,Number=1,Type=Float,Description="Allele Frequency for samples from AMR based on AC/AN">
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##INFO=<ID=AN,Number=1,Type=Integer,Description="Total Allele Count">
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##INFO=<ID=ASN_AF,Number=1,Type=Float,Description="Allele Frequency for samples from ASN based on AC/AN">
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##INFO=<ID=AVGPOST,Number=1,Type=Float,Description="Average posterior probability from MaCH/Thunder">
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##INFO=<ID=CIEND,Number=2,Type=Integer,Description="Confidence interval around END for imprecise variants">
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##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS for imprecise variants">
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##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
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##INFO=<ID=ERATE,Number=1,Type=Float,Description="Per-marker Mutation rate from MaCH/Thunder">
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##INFO=<ID=EUR_AF,Number=1,Type=Float,Description="Allele Frequency for samples from EUR based on AC/AN">
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##INFO=<ID=HOMLEN,Number=.,Type=Integer,Description="Length of base pair identical micro-homology at event breakpoints">
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##INFO=<ID=HOMSEQ,Number=.,Type=String,Description="Sequence of base pair identical micro-homology at event breakpoints">
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##INFO=<ID=LDAF,Number=1,Type=Float,Description="MLE Allele Frequency Accounting for LD">
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##INFO=<ID=RSQ,Number=1,Type=Float,Description="Genotype imputation quality from MaCH/Thunder">
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##INFO=<ID=SNPSOURCE,Number=.,Type=String,Description="indicates if a snp was called when analysing the low coverage or exome alignment data">
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##INFO=<ID=SVLEN,Number=1,Type=Integer,Description="Difference in length between REF and ALT alleles">
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##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
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##INFO=<ID=THETA,Number=1,Type=Float,Description="Per-marker Transition rate from MaCH/Thunder">
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##INFO=<ID=VT,Number=1,Type=String,Description="indicates what type of variant the line represents">
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##SelectVariants="analysis_type=SelectVariants input_file=[] read_buffer_size=null phone_home=STANDARD gatk_key=null read_filter=[] intervals=[20:81006] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL reference_sequence=/humgen/gsa-hpprojects/GATK/bundle/current/b37/human_g1k_v37.fasta rodBind=[] nonDeterministicRandomSeed=false downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false BQSR=null defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 num_cpu_threads=null num_io_threads=null num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false logging_level=INFO log_to_file=null help=false variant=(RodBinding name=variant source=/humgen/1kg/releases/main_project_phaseI/ALL.chr20.phase1_release_v3.20101123.snps_indels_svs.genotypes.vcf.gz) discordance=(RodBinding name= source=UNBOUND) concordance=(RodBinding name= source=UNBOUND) out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sample_name=[] sample_expressions=null sample_file=null exclude_sample_name=[] exclude_sample_file=[] select_expressions=[] excludeNonVariants=false excludeFiltered=false restrictAllelesTo=ALL keepOriginalAC=false mendelianViolation=false mendelianViolationQualThreshold=0.0 select_random_number=0 select_random_fraction=0.0 remove_fraction_genotypes=0.0 selectTypeToInclude=[] keepIDs=null outMVFile=null filter_mismatching_base_and_quals=false"
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##contig=<ID=1,length=249250621,assembly=b37>
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##contig=<ID=10,length=135534747,assembly=b37>
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##contig=<ID=11,length=135006516,assembly=b37>
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##contig=<ID=12,length=133851895,assembly=b37>
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##contig=<ID=13,length=115169878,assembly=b37>
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##contig=<ID=14,length=107349540,assembly=b37>
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##contig=<ID=15,length=102531392,assembly=b37>
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##contig=<ID=16,length=90354753,assembly=b37>
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##contig=<ID=17,length=81195210,assembly=b37>
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##contig=<ID=18,length=78077248,assembly=b37>
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##contig=<ID=19,length=59128983,assembly=b37>
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##contig=<ID=2,length=243199373,assembly=b37>
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##contig=<ID=20,length=63025520,assembly=b37>
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##contig=<ID=21,length=48129895,assembly=b37>
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##contig=<ID=22,length=51304566,assembly=b37>
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##contig=<ID=3,length=198022430,assembly=b37>
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##contig=<ID=4,length=191154276,assembly=b37>
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##contig=<ID=5,length=180915260,assembly=b37>
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##contig=<ID=6,length=171115067,assembly=b37>
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##contig=<ID=7,length=159138663,assembly=b37>
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##contig=<ID=8,length=146364022,assembly=b37>
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##contig=<ID=9,length=141213431,assembly=b37>
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##contig=<ID=GL000191.1,length=106433,assembly=b37>
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##contig=<ID=GL000192.1,length=547496,assembly=b37>
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##contig=<ID=GL000193.1,length=189789,assembly=b37>
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##contig=<ID=GL000194.1,length=191469,assembly=b37>
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##contig=<ID=GL000195.1,length=182896,assembly=b37>
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##contig=<ID=GL000196.1,length=38914,assembly=b37>
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##contig=<ID=GL000197.1,length=37175,assembly=b37>
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##contig=<ID=GL000198.1,length=90085,assembly=b37>
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##contig=<ID=GL000199.1,length=169874,assembly=b37>
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##contig=<ID=GL000200.1,length=187035,assembly=b37>
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##contig=<ID=GL000201.1,length=36148,assembly=b37>
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##contig=<ID=GL000202.1,length=40103,assembly=b37>
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##contig=<ID=GL000203.1,length=37498,assembly=b37>
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##contig=<ID=GL000204.1,length=81310,assembly=b37>
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##contig=<ID=GL000205.1,length=174588,assembly=b37>
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##contig=<ID=GL000206.1,length=41001,assembly=b37>
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##contig=<ID=GL000207.1,length=4262,assembly=b37>
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##contig=<ID=GL000208.1,length=92689,assembly=b37>
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##contig=<ID=GL000209.1,length=159169,assembly=b37>
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##contig=<ID=GL000210.1,length=27682,assembly=b37>
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##contig=<ID=GL000211.1,length=166566,assembly=b37>
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##contig=<ID=GL000213.1,length=164239,assembly=b37>
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##contig=<ID=GL000214.1,length=137718,assembly=b37>
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##contig=<ID=GL000215.1,length=172545,assembly=b37>
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##contig=<ID=GL000216.1,length=172294,assembly=b37>
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##contig=<ID=GL000217.1,length=172149,assembly=b37>
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##contig=<ID=GL000218.1,length=161147,assembly=b37>
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##contig=<ID=GL000219.1,length=179198,assembly=b37>
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##contig=<ID=GL000220.1,length=161802,assembly=b37>
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##contig=<ID=GL000221.1,length=155397,assembly=b37>
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##contig=<ID=GL000222.1,length=186861,assembly=b37>
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##contig=<ID=GL000223.1,length=180455,assembly=b37>
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##contig=<ID=GL000224.1,length=179693,assembly=b37>
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##contig=<ID=GL000225.1,length=211173,assembly=b37>
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##contig=<ID=GL000226.1,length=15008,assembly=b37>
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##contig=<ID=GL000227.1,length=128374,assembly=b37>
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##contig=<ID=GL000228.1,length=129120,assembly=b37>
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##contig=<ID=GL000229.1,length=19913,assembly=b37>
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##contig=<ID=GL000230.1,length=43691,assembly=b37>
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##contig=<ID=GL000231.1,length=27386,assembly=b37>
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##contig=<ID=GL000232.1,length=40652,assembly=b37>
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##contig=<ID=GL000233.1,length=45941,assembly=b37>
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##contig=<ID=GL000234.1,length=40531,assembly=b37>
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##contig=<ID=GL000235.1,length=34474,assembly=b37>
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##contig=<ID=GL000236.1,length=41934,assembly=b37>
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##contig=<ID=GL000237.1,length=45867,assembly=b37>
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##contig=<ID=GL000238.1,length=39939,assembly=b37>
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##contig=<ID=GL000239.1,length=33824,assembly=b37>
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##contig=<ID=GL000240.1,length=41933,assembly=b37>
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##contig=<ID=GL000241.1,length=42152,assembly=b37>
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##contig=<ID=GL000242.1,length=43523,assembly=b37>
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##contig=<ID=GL000243.1,length=43341,assembly=b37>
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##contig=<ID=GL000244.1,length=39929,assembly=b37>
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##contig=<ID=GL000245.1,length=36651,assembly=b37>
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##contig=<ID=GL000248.1,length=39786,assembly=b37>
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##contig=<ID=GL000249.1,length=38502,assembly=b37>
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##contig=<ID=MT,length=16569,assembly=b37>
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##contig=<ID=X,length=155270560,assembly=b37>
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##contig=<ID=Y,length=59373566,assembly=b37>
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##reference=file:///humgen/gsa-hpprojects/GATK/bundle/current/b37/human_g1k_v37.fasta
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##source=SelectVariants
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#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG00096 HG00097 HG00099 HG00100 HG00101 HG00102 HG00103 HG00104 HG00106 HG00108 HG00109 HG00110 HG00111 HG00112 HG00113 HG00114 HG00116 HG00117 HG00118 HG00119 HG00120 HG00121 HG00122 HG00123 HG00124 HG00125 HG00126 HG00127 HG00128 HG00129 HG00130 HG00131 HG00133 HG00134 HG00135 HG00136 HG00137 HG00138 HG00139 HG00140 HG00141 HG00142 HG00143 HG00146 HG00148 HG00149 HG00150 HG00151 HG00152 HG00154 HG00155 HG00156 HG00158 HG00159 HG00160 HG00171 HG00173 HG00174 HG00176 HG00177 HG00178 HG00179 HG00180 HG00182 HG00183 HG00185 HG00186 HG00187 HG00188 HG00189 HG00190 HG00231 HG00232 HG00233 HG00234 HG00235 HG00236 HG00237 HG00238 HG00239 HG00240 HG00242 HG00243 HG00244 HG00245 HG00246 HG00247 HG00249 HG00250 HG00251 HG00252 HG00253 HG00254 HG00255 HG00256 HG00257 HG00258 HG00259 HG00260 HG00261 HG00262 HG00263 HG00264 HG00265 HG00266 HG00267 HG00268 HG00269 HG00270 HG00271 HG00272 HG00273 HG00274 HG00275 HG00276 HG00277 HG00278 HG00280 HG00281 HG00282 HG00284 HG00285 HG00306 HG00309 HG00310 HG00311 HG00312 HG00313 HG00315 HG00318 HG00319 HG00320 HG00321 HG00323 HG00324 HG00325 HG00326 HG00327 HG00328 HG00329 HG00330 HG00331 HG00332 HG00334 HG00335 HG00336 HG00337 HG00338 HG00339 HG00341 HG00342 HG00343 HG00344 HG00345 HG00346 HG00349 HG00350 HG00351 HG00353 HG00355 HG00356 HG00357 HG00358 HG00359 HG00360 HG00361 HG00362 HG00364 HG00366 HG00367 HG00369 HG00372 HG00373 HG00375 HG00376 HG00377 HG00378 HG00381 HG00382 HG00383 HG00384 HG00403 HG00404 HG00406 HG00407 HG00418 HG00419 HG00421 HG00422 HG00427 HG00428 HG00436 HG00437 HG00442 HG00443 HG00445 HG00446 HG00448 HG00449 HG00451 HG00452 HG00457 HG00458 HG00463 HG00464 HG00472 HG00473 HG00475 HG00476 HG00478 HG00479 HG00500 HG00501 HG00512 HG00513 HG00524 HG00525 HG00530 HG00531 HG00533 HG00534 HG00536 HG00537 HG00542 HG00543 HG00553 HG00554 HG00556 HG00557 HG00559 HG00560 HG00565 HG00566 HG00577 HG00578 HG00580 HG00581 HG00583 HG00584 HG00589 HG00590 HG00592 HG00593 HG00595 HG00596 HG00607 HG00608 HG00610 HG00611 HG00613 HG00614 HG00619 HG00620 HG00625 HG00626 HG00628 HG00629 HG00634 HG00635 HG00637 HG00638 HG00640 HG00641 HG00650 HG00651 HG00653 HG00654 HG00656 HG00657 HG00662 HG00663 HG00671 HG00672 HG00683 HG00684 HG00689 HG00690 HG00692 HG00693 HG00698 HG00699 HG00701 HG00702 HG00704 HG00705 HG00707 HG00708 HG00731 HG00732 HG00734 HG00736 HG00737 HG00740 HG01047 HG01048 HG01051 HG01052 HG01055 HG01060 HG01061 HG01066 HG01067 HG01069 HG01070 HG01072 HG01073 HG01075 HG01079 HG01080 HG01082 HG01083 HG01085 HG01095 HG01097 HG01098 HG01101 HG01102 HG01104 HG01105 HG01107 HG01108 HG01112 HG01113 HG01124 HG01125 HG01133 HG01134 HG01136 HG01137 HG01140 HG01148 HG01149 HG01167 HG01168 HG01170 HG01171 HG01173 HG01174 HG01176 HG01183 HG01187 HG01188 HG01190 HG01191 HG01197 HG01198 HG01204 HG01250 HG01251 HG01257 HG01259 HG01271 HG01272 HG01274 HG01275 HG01277 HG01278 HG01334 HG01342 HG01344 HG01345 HG01350 HG01351 HG01353 HG01354 HG01356 HG01357 HG01359 HG01360 HG01365 HG01366 HG01374 HG01375 HG01377 HG01378 HG01383 HG01384 HG01389 HG01390 HG01437 HG01440 HG01441 HG01455 HG01456 HG01461 HG01462 HG01465 HG01488 HG01489 HG01491 HG01492 HG01494 HG01495 HG01497 HG01498 HG01515 HG01516 HG01518 HG01519 HG01521 HG01522 HG01550 HG01551 HG01617 HG01618 HG01619 HG01620 HG01623 HG01624 HG01625 HG01626 NA06984 NA06986 NA06989 NA06994 NA07000 NA07037 NA07048 NA07051 NA07056 NA07347 NA07357 NA10847 NA10851 NA11829 NA11830 NA11831 NA11843 NA11892 NA11893 NA11894 NA11919 NA11920 NA11930 NA11931 NA11932 NA11933 NA11992 NA11993 NA11994 NA11995 NA12003 NA12004 NA12006 NA12043 NA12044 NA12045 NA12046 NA12058 NA12144 NA12154 NA12155 NA12249 NA12272 NA12273 NA12275 NA12282 NA12283 NA12286 NA12287 NA12340 NA12341 NA12342 NA12347 NA12348 NA12383 NA12399 NA12400 NA12413 NA12489 NA12546 NA12716 NA12717 NA12718 NA12748 NA12749 NA12750 NA12751 NA12761 NA12763 NA12775 NA12777 NA12778 NA12812 NA12814 NA12815 NA12827 NA12829 NA12830 NA12842 NA12843 NA12872 NA12873 NA12874 NA12889 NA12890 NA18486 NA18487 NA18489 NA18498 NA18499 NA18501 NA18502 NA18504 NA18505 NA18507 N
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