Mercurial > repos > bgruening > vt
view test-data/decompose_result01.vcf @ 0:26babe3a66f1 draft default tip
planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
| author | bgruening |
|---|---|
| date | Sat, 04 Jun 2016 10:41:29 -0400 |
| parents | |
| children |
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##fileformat=VCFv4.0 ##FILTER=<ID=PASS,Description="All filters passed"> ##contig=<ID=1,length=249250621,assembly=b37> ##contig=<ID=2,length=243199373,assembly=b37> ##contig=<ID=3,length=198022430,assembly=b37> ##contig=<ID=4,length=191154276,assembly=b37> ##contig=<ID=5,length=180915260,assembly=b37> ##contig=<ID=6,length=171115067,assembly=b37> ##contig=<ID=7,length=159138663,assembly=b37> ##contig=<ID=8,length=146364022,assembly=b37> ##contig=<ID=9,length=141213431,assembly=b37> ##contig=<ID=10,length=135534747,assembly=b37> ##contig=<ID=11,length=135006516,assembly=b37> ##contig=<ID=12,length=133851895,assembly=b37> ##contig=<ID=13,length=115169878,assembly=b37> ##contig=<ID=14,length=107349540,assembly=b37> ##contig=<ID=15,length=102531392,assembly=b37> ##contig=<ID=16,length=90354753,assembly=b37> ##contig=<ID=17,length=81195210,assembly=b37> ##contig=<ID=18,length=78077248,assembly=b37> ##contig=<ID=19,length=59128983,assembly=b37> ##contig=<ID=20,length=63025520,assembly=b37> ##contig=<ID=21,length=48129895,assembly=b37> ##contig=<ID=22,length=51304566,assembly=b37> ##contig=<ID=X,length=155270560,assembly=b37> ##contig=<ID=Y,length=59373566,assembly=b37> ##contig=<ID=MT,length=16569,assembly=b37> ##contig=<ID=GL000207.1,length=4262,assembly=b37> ##contig=<ID=GL000226.1,length=15008,assembly=b37> ##contig=<ID=GL000229.1,length=19913,assembly=b37> ##contig=<ID=GL000231.1,length=27386,assembly=b37> ##contig=<ID=GL000210.1,length=27682,assembly=b37> ##contig=<ID=GL000239.1,length=33824,assembly=b37> ##contig=<ID=GL000235.1,length=34474,assembly=b37> ##contig=<ID=GL000201.1,length=36148,assembly=b37> ##contig=<ID=GL000247.1,length=36422,assembly=b37> ##contig=<ID=GL000245.1,length=36651,assembly=b37> ##contig=<ID=GL000197.1,length=37175,assembly=b37> ##contig=<ID=GL000203.1,length=37498,assembly=b37> ##contig=<ID=GL000246.1,length=38154,assembly=b37> ##contig=<ID=GL000249.1,length=38502,assembly=b37> ##contig=<ID=GL000196.1,length=38914,assembly=b37> ##contig=<ID=GL000248.1,length=39786,assembly=b37> ##contig=<ID=GL000244.1,length=39929,assembly=b37> ##contig=<ID=GL000238.1,length=39939,assembly=b37> ##contig=<ID=GL000202.1,length=40103,assembly=b37> ##contig=<ID=GL000234.1,length=40531,assembly=b37> ##contig=<ID=GL000232.1,length=40652,assembly=b37> ##contig=<ID=GL000206.1,length=41001,assembly=b37> ##contig=<ID=GL000240.1,length=41933,assembly=b37> ##contig=<ID=GL000236.1,length=41934,assembly=b37> ##contig=<ID=GL000241.1,length=42152,assembly=b37> ##contig=<ID=GL000243.1,length=43341,assembly=b37> ##contig=<ID=GL000242.1,length=43523,assembly=b37> ##contig=<ID=GL000230.1,length=43691,assembly=b37> ##contig=<ID=GL000237.1,length=45867,assembly=b37> ##contig=<ID=GL000233.1,length=45941,assembly=b37> ##contig=<ID=GL000204.1,length=81310,assembly=b37> ##contig=<ID=GL000198.1,length=90085,assembly=b37> ##contig=<ID=GL000208.1,length=92689,assembly=b37> ##contig=<ID=GL000191.1,length=106433,assembly=b37> ##contig=<ID=GL000227.1,length=128374,assembly=b37> ##contig=<ID=GL000228.1,length=129120,assembly=b37> ##contig=<ID=GL000214.1,length=137718,assembly=b37> ##contig=<ID=GL000221.1,length=155397,assembly=b37> ##contig=<ID=GL000209.1,length=159169,assembly=b37> ##contig=<ID=GL000218.1,length=161147,assembly=b37> ##contig=<ID=GL000220.1,length=161802,assembly=b37> ##contig=<ID=GL000213.1,length=164239,assembly=b37> ##contig=<ID=GL000211.1,length=166566,assembly=b37> ##contig=<ID=GL000199.1,length=169874,assembly=b37> ##contig=<ID=GL000217.1,length=172149,assembly=b37> ##contig=<ID=GL000216.1,length=172294,assembly=b37> ##contig=<ID=GL000215.1,length=172545,assembly=b37> ##contig=<ID=GL000205.1,length=174588,assembly=b37> ##contig=<ID=GL000219.1,length=179198,assembly=b37> ##contig=<ID=GL000224.1,length=179693,assembly=b37> ##contig=<ID=GL000223.1,length=180455,assembly=b37> ##contig=<ID=GL000195.1,length=182896,assembly=b37> ##contig=<ID=GL000212.1,length=186858,assembly=b37> ##contig=<ID=GL000222.1,length=186861,assembly=b37> ##contig=<ID=GL000200.1,length=187035,assembly=b37> ##contig=<ID=GL000193.1,length=189789,assembly=b37> ##contig=<ID=GL000194.1,length=191469,assembly=b37> ##contig=<ID=GL000225.1,length=211173,assembly=b37> ##contig=<ID=GL000192.1,length=547496,assembly=b37> ##FilterLiftedVariants="analysis_type=FilterLiftedVariants input_file=[] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=null excludeIntervals=null reference_sequence=/local/sequence/reference/BWA_ref/hg19/hg19.fasta rodBind=[/local/scratch/xyliu/0.915136538286792.sorted.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false enable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null quiet_output_mode=false debug_mode=false help=false 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" ##INFO=<ID=VC,Number=1,Type=String,Description="Variation Class"> ##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed"> ##INFO=<ID=AF,Number=.,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=DB,Number=0,Type=Flag,Description="dbSNP Membership"> ##INFO=<ID=refseq.name,Number=1,Type=String,Description="RefSeq name"> ##INFO=<ID=refseq.positionType,Number=1,Type=String,Description="RefSeq genome type position"> ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> ##INFO=<ID=OLD_MULTIALLELIC,Number=1,Type=String,Description="Original chr:pos:ref:alt encoding"> #CHROM POS ID REF ALT QUAL FILTER INFO 20 421808 . A ACCA . PASS VC=INDEL;AC=24;AF=0.08;AN=316;refseq.name=NM_144628;refseq.positionType=intron 20 1292033 . C CTTGT . PASS VC=INDEL;AC=28;AF=0.1;AN=276;refseq.name=NM_080489;refseq.positionType=intron 20 1340527 . T TGTC . PASS VC=INDEL;AC=56;AF=0.18;AN=316 20 1600125 . GAA G . PASS VC=INDEL;AC=3;AF=0.01;AN=312;refseq.name=NM_001083910;refseq.positionType=intron 20 1728298 . G GT . PASS VC=INDEL;AC=199;AF=0.63;AN=316 20 2171402 . T TA . PASS VC=INDEL;AC=223;AF=0.71;AN=316 20 2171404 . A AA . PASS VC=INDEL;AC=223;AF=0.71;AN=316 20 2982245 . CT C . PASS VC=INDEL;AC=118;AF=0.38;AN=314;refseq.name=NM_002836;refseq.positionType=intron 20 3025866 . TCAAA T . PASS VC=INDEL;AC=31;AF=0.1;AN=306;refseq.name=NM_001501;refseq.positionType=intron 20 3373441 . TCTTT T . PASS VC=INDEL;AC=58;AF=0.18;AN=316;refseq.name=NM_001009984;refseq.positionType=intron 20 3635159 . T TT . PASS VC=INDEL;AC=130;AF=0.47;AN=274 20 4422119 . GCTCCCAGGCTACAGAAAGATGATGGAG G . PASS VC=INDEL;AC=174;AF=0.55;AN=314 20 5151108 . GTTCT G . PASS VC=INDEL;AC=61;AF=0.2;AN=304;refseq.name=NM_003818;refseq.positionType=intron 20 5280839 . T TATA . PASS VC=INDEL;AC=202;AF=0.75;AN=268 20 5291223 . TCAG T . PASS VC=INDEL;AC=51;AF=0.16;AN=316;refseq.name=NM_144773;refseq.positionType=intron 20 5509358 . T TG . PASS VC=INDEL;AC=136;AF=0.43;AN=316 20 5900669 . G GC . PASS VC=INDEL;AC=69;AF=0.23;AN=300;refseq.name=NM_001819;refseq.positionType=intron 20 5900670 . C CC . PASS VC=INDEL;AC=68;AF=0.22;AN=304;refseq.name=NM_001819;refseq.positionType=intron 20 6351757 . C CTT . PASS VC=INDEL;AC=52;AF=0.17;AN=314 20 6362163 . GC G . PASS VC=INDEL;AC=49;AF=0.2;AN=250 20 6481086 . T TTGTC . PASS VC=INDEL;AC=307;AF=0.97;AN=316 20 8080280 . GTTTG G . PASS VC=INDEL;AC=118;AF=0.37;AN=316 20 8781394 . AA A . PASS VC=INDEL;AC=122;AF=0.39;AN=316;refseq.name=NM_015192;refseq.positionType=intron 20 8833756 . TT T . PASS VC=INDEL;AC=13;AF=0.04;AN=298;refseq.name=NM_015192;refseq.positionType=intron 20 9035330 . T TT . PASS VC=INDEL;AC=110;AF=0.35;AN=314 20 9311904 . TGTATCTGTCCA T . PASS VC=INDEL;AC=46;AF=0.15;AN=314;refseq.name=NM_000933;refseq.positionType=intron 20 9389232 . GGGTTTGAT G . PASS VC=INDEL;AC=77;AF=0.25;AN=306;refseq.name=NM_000933;refseq.positionType=intron