Mercurial > repos > hepcat72 > vcfsamplecompare
comparison test-data/test10.in3.s0.d0.af.a6.hy.fy.gy.vcf @ 0:cdd7fecae37c draft
planemo upload commit c786cb50e512783d81d4a9ad57add9151ac5904f
| author | hepcat72 |
|---|---|
| date | Wed, 10 Oct 2018 18:53:14 -0400 |
| parents | |
| children |
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| -1:000000000000 | 0:cdd7fecae37c |
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| 1 ##fileformat=VCFv4.2 | |
| 2 ##fileDate=20180104 | |
| 3 ##reference= | |
| 4 ##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant"> | |
| 5 ##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles"> | |
| 6 ##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record"> | |
| 7 ##INFO=<ID=STRANDS,Number=.,Type=String,Description="Strand orientation of the adjacency in BEDPE format (DEL:+-, DUP:-+, INV:++/--)"> | |
| 8 ##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation"> | |
| 9 ##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS for imprecise variants"> | |
| 10 ##INFO=<ID=CIEND,Number=2,Type=Integer,Description="Confidence interval around END for imprecise variants"> | |
| 11 ##INFO=<ID=CIPOS95,Number=2,Type=Integer,Description="Confidence interval (95%) around POS for imprecise variants"> | |
| 12 ##INFO=<ID=CIEND95,Number=2,Type=Integer,Description="Confidence interval (95%) around END for imprecise variants"> | |
| 13 ##INFO=<ID=MATEID,Number=.,Type=String,Description="ID of mate breakends"> | |
| 14 ##INFO=<ID=EVENT,Number=1,Type=String,Description="ID of event associated to breakend"> | |
| 15 ##INFO=<ID=SECONDARY,Number=0,Type=Flag,Description="Secondary breakend in a multi-line variants"> | |
| 16 ##INFO=<ID=SU,Number=.,Type=Integer,Description="Number of pieces of evidence supporting the variant across all samples"> | |
| 17 ##INFO=<ID=PE,Number=.,Type=Integer,Description="Number of paired-end reads supporting the variant across all samples"> | |
| 18 ##INFO=<ID=SR,Number=.,Type=Integer,Description="Number of split reads supporting the variant across all samples"> | |
| 19 ##INFO=<ID=BD,Number=.,Type=Integer,Description="Amount of BED evidence supporting the variant across all samples"> | |
| 20 ##INFO=<ID=EV,Number=.,Type=String,Description="Type of LUMPY evidence contributing to the variant call"> | |
| 21 ##INFO=<ID=PRPOS,Number=.,Type=String,Description="LUMPY probability curve of the POS breakend"> | |
| 22 ##INFO=<ID=PREND,Number=.,Type=String,Description="LUMPY probability curve of the END breakend"> | |
| 23 ##ALT=<ID=DEL,Description="Deletion"> | |
| 24 ##ALT=<ID=DUP,Description="Duplication"> | |
| 25 ##ALT=<ID=INV,Description="Inversion"> | |
| 26 ##ALT=<ID=DUP:TANDEM,Description="Tandem duplication"> | |
| 27 ##ALT=<ID=INS,Description="Insertion of novel sequence"> | |
| 28 ##ALT=<ID=CNV,Description="Copy number variable region"> | |
| 29 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> | |
| 30 ##FORMAT=<ID=SU,Number=1,Type=Integer,Description="Number of pieces of evidence supporting the variant"> | |
| 31 ##FORMAT=<ID=PE,Number=1,Type=Integer,Description="Number of paired-end reads supporting the variant"> | |
| 32 ##FORMAT=<ID=SR,Number=1,Type=Integer,Description="Number of split reads supporting the variant"> | |
| 33 ##FORMAT=<ID=BD,Number=1,Type=Integer,Description="Amount of BED evidence supporting the variant"> | |
| 34 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype quality"> | |
| 35 ##FORMAT=<ID=SQ,Number=1,Type=Float,Description="Phred-scaled probability that this site is variant (non-reference in this sample"> | |
| 36 ##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy"> | |
| 37 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth"> | |
| 38 ##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count, with partial observations recorded fractionally"> | |
| 39 ##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observations, with partial observations recorded fractionally"> | |
| 40 ##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of reference observations"> | |
| 41 ##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of alternate observations"> | |
| 42 ##FORMAT=<ID=RS,Number=1,Type=Integer,Description="Reference allele split-read observation count, with partial observations recorded fractionally"> | |
| 43 ##FORMAT=<ID=AS,Number=A,Type=Integer,Description="Alternate allele split-read observation count, with partial observations recorded fractionally"> | |
| 44 ##FORMAT=<ID=ASC,Number=A,Type=Integer,Description="Alternate allele clipped-read observation count, with partial observations recorded fractionally"> | |
| 45 ##FORMAT=<ID=RP,Number=1,Type=Integer,Description="Reference allele paired-end observation count, with partial observations recorded fractionally"> | |
| 46 ##FORMAT=<ID=AP,Number=A,Type=Integer,Description="Alternate allele paired-end observation count, with partial observations recorded fractionally"> | |
| 47 ##FORMAT=<ID=AB,Number=A,Type=Float,Description="Allele balance, fraction of observations from alternate allele, QA/(QR+QA)"> | |
| 48 ##source=LUMPY | |
| 49 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 195 213 | |
| 50 chr1 1659220 6 N <DUP> 13154.05 . SVTYPE=DUP;SVLEN=6530;END=1665750;STRANDS=-+:627;CIPOS=0,0;CIEND=0,0;CIPOS95=0,0;CIEND95=0,0;SU=627;PE=482;SR=145 GT:SU:PE:SR:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB 1/1:627:482:145:200:13154.05:-1452,-264,-136:890:97:792:96:791:43:144:129:53:517:0.89 0/0:0:0:0:151:0.00:-0,-16,-27:90:90:0:89:0:42:0:0:47:0:0 |