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planemo upload for repository https://github.com/atks/vt commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472-dirty
author bgruening
date Sat, 04 Jun 2016 12:44:06 -0400
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Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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7c2ef0170f03 planemo upload for repository https://github.com/atks/vt commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472-dirty
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86 ##contig=<ID=GL000192.1,length=547496,assembly=b37>
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87 ##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"
7c2ef0170f03 planemo upload for repository https://github.com/atks/vt commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472-dirty
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88 ##INFO=<ID=VC,Number=1,Type=String,Description="Variation Class">
7c2ef0170f03 planemo upload for repository https://github.com/atks/vt commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472-dirty
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89 ##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
7c2ef0170f03 planemo upload for repository https://github.com/atks/vt commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472-dirty
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90 ##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
7c2ef0170f03 planemo upload for repository https://github.com/atks/vt commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472-dirty
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91 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
7c2ef0170f03 planemo upload for repository https://github.com/atks/vt commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472-dirty
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92 ##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP Membership">
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93 ##INFO=<ID=refseq.name,Number=1,Type=String,Description="RefSeq name">
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94 ##INFO=<ID=refseq.positionType,Number=1,Type=String,Description="RefSeq genome type position">
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95 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
7c2ef0170f03 planemo upload for repository https://github.com/atks/vt commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472-dirty
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96 ##INFO=<ID=OLD_VARIANT,Number=.,Type=String,Description="Original chr:pos:ref:alt encoding">
7c2ef0170f03 planemo upload for repository https://github.com/atks/vt commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472-dirty
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97 #CHROM POS ID REF ALT QUAL FILTER INFO
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98 20 421805 . T TCCA . PASS VC=INDEL;AC=24;AF=0.08;AN=316;refseq.name=NM_144628;refseq.positionType=intron;OLD_VARIANT=20:421808:A/ACCA
7c2ef0170f03 planemo upload for repository https://github.com/atks/vt commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472-dirty
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99 20 1292033 . C CTTGT . PASS VC=INDEL;AC=28;AF=0.1;AN=276;refseq.name=NM_080489;refseq.positionType=intron
7c2ef0170f03 planemo upload for repository https://github.com/atks/vt commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472-dirty
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100 20 1340527 . T TGTC . PASS VC=INDEL;AC=56;AF=0.18;AN=316
7c2ef0170f03 planemo upload for repository https://github.com/atks/vt commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472-dirty
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101 20 1600125 . GAA G . PASS VC=INDEL;AC=3;AF=0.01;AN=312;refseq.name=NM_001083910;refseq.positionType=intron
7c2ef0170f03 planemo upload for repository https://github.com/atks/vt commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472-dirty
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102 20 1728298 . G GT . PASS VC=INDEL;AC=199;AF=0.63;AN=316
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103 20 2171402 . T TA . PASS VC=INDEL;AC=223;AF=0.71;AN=316
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104 20 2171402 . T TA . PASS VC=INDEL;AC=223;AF=0.71;AN=316;OLD_VARIANT=20:2171404:A/AA
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105 20 2982245 . CT C . PASS VC=INDEL;AC=118;AF=0.38;AN=314;refseq.name=NM_002836;refseq.positionType=intron
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106 20 3025866 . TCAAA T . PASS VC=INDEL;AC=31;AF=0.1;AN=306;refseq.name=NM_001501;refseq.positionType=intron
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107 20 3373437 . GCTTT G . PASS VC=INDEL;AC=58;AF=0.18;AN=316;refseq.name=NM_001009984;refseq.positionType=intron;OLD_VARIANT=20:3373441:TCTTT/T
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108 20 3635158 . A AT . PASS VC=INDEL;AC=130;AF=0.47;AN=274;OLD_VARIANT=20:3635159:T/TT
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109 20 4422115 . GGGAGCTCCCAGGCTACAGAAAGATGAT G . PASS VC=INDEL;AC=174;AF=0.55;AN=314;OLD_VARIANT=20:4422119:GCTCCCAGGCTACAGAAAGATGATGGAG/G
7c2ef0170f03 planemo upload for repository https://github.com/atks/vt commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472-dirty
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110 20 5151108 . GTTCT G . PASS VC=INDEL;AC=61;AF=0.2;AN=304;refseq.name=NM_003818;refseq.positionType=intron
7c2ef0170f03 planemo upload for repository https://github.com/atks/vt commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472-dirty
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111 20 5280839 . T TATA . PASS VC=INDEL;AC=202;AF=0.75;AN=268
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112 20 5291223 . TCAG T . PASS VC=INDEL;AC=51;AF=0.16;AN=316;refseq.name=NM_144773;refseq.positionType=intron
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113 20 5509358 . T TG . PASS VC=INDEL;AC=136;AF=0.43;AN=316
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114 20 5900669 . G GC . PASS VC=INDEL;AC=69;AF=0.23;AN=300;refseq.name=NM_001819;refseq.positionType=intron
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115 20 5900669 . G GC . PASS VC=INDEL;AC=68;AF=0.22;AN=304;refseq.name=NM_001819;refseq.positionType=intron;OLD_VARIANT=20:5900670:C/CC
7c2ef0170f03 planemo upload for repository https://github.com/atks/vt commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472-dirty
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116 20 6351757 . C CTT . PASS VC=INDEL;AC=52;AF=0.17;AN=314
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117 20 6362163 . GC G . PASS VC=INDEL;AC=49;AF=0.2;AN=250
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118 20 6481086 . T TTGTC . PASS VC=INDEL;AC=307;AF=0.97;AN=316
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119 20 8080280 . GTTTG G . PASS VC=INDEL;AC=118;AF=0.37;AN=316
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120 20 8781394 . AA A . PASS VC=INDEL;AC=122;AF=0.39;AN=316;refseq.name=NM_015192;refseq.positionType=intron
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121 20 7391879 . C CT . PASS VC=INDEL;AC=110;AF=0.35;AN=314;OLD_VARIANT=20:9035330:T/TT
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122 20 8833756 . TT T . PASS VC=INDEL;AC=13;AF=0.04;AN=298;refseq.name=NM_015192;refseq.positionType=intron
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123 20 9311904 . TGTATCTGTCCA T . PASS VC=INDEL;AC=46;AF=0.15;AN=314;refseq.name=NM_000933;refseq.positionType=intron
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124 20 9389232 . GGGTTTGAT G . PASS VC=INDEL;AC=77;AF=0.25;AN=306;refseq.name=NM_000933;refseq.positionType=intron