Mercurial > repos > bgruening > vt_decompose
view test-data/infile02.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 |
| 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> 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##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 1 3759889 . TA TAA,TAAA,T . PASS AF=0.342,0.173,0.037 GT:DP:PL 1/2:81:281,5,9,58,0,115,338,46,116,809 0/0:86:0,30,323,31,365,483,38,291,325,567