view test-data/decompose_result02.vcf @ 0:490e605d1f44 draft default tip

planemo upload for repository https://github.com/atks/vt commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472-dirty
author bgruening
date Sat, 04 Jun 2016 12:45:04 -0400
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##fileformat=VCFv4.0
##FILTER=<ID=PASS,Description="All filters passed">
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##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">
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##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
1	3759889	.	TA	TAA	.	PASS	AF=0.342,0.173,0.037;OLD_MULTIALLELIC=1:3759889:TA/TAA/TAAA/T
1	3759889	.	TA	TAAA	.	PASS	AF=0.342,0.173,0.037;OLD_MULTIALLELIC=1:3759889:TA/TAA/TAAA/T
1	3759889	.	TA	T	.	PASS	AF=0.342,0.173,0.037;OLD_MULTIALLELIC=1:3759889:TA/TAA/TAAA/T