Mercurial > repos > artbio > lumpy_sv
comparison test-data/output.vcf @ 0:796552c157de draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy-sv commit d06124e8a097f3f665b4955281f40fe811eaee64
| author | artbio |
|---|---|
| date | Mon, 24 Jul 2017 08:03:17 -0400 |
| parents | |
| children |
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| -1:000000000000 | 0:796552c157de |
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| 1 ##fileformat=VCFv4.2 | |
| 2 ##source=LUMPY | |
| 3 ##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant"> | |
| 4 ##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles"> | |
| 5 ##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record"> | |
| 6 ##INFO=<ID=STRANDS,Number=.,Type=String,Description="Strand orientation of the adjacency in BEDPE format (DEL:+-, DUP:-+, INV:++/--)"> | |
| 7 ##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation"> | |
| 8 ##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS for imprecise variants"> | |
| 9 ##INFO=<ID=CIEND,Number=2,Type=Integer,Description="Confidence interval around END for imprecise variants"> | |
| 10 ##INFO=<ID=CIPOS95,Number=2,Type=Integer,Description="Confidence interval (95%) around POS for imprecise variants"> | |
| 11 ##INFO=<ID=CIEND95,Number=2,Type=Integer,Description="Confidence interval (95%) around END for imprecise variants"> | |
| 12 ##INFO=<ID=MATEID,Number=.,Type=String,Description="ID of mate breakends"> | |
| 13 ##INFO=<ID=EVENT,Number=1,Type=String,Description="ID of event associated to breakend"> | |
| 14 ##INFO=<ID=SECONDARY,Number=0,Type=Flag,Description="Secondary breakend in a multi-line variants"> | |
| 15 ##INFO=<ID=SU,Number=.,Type=Integer,Description="Number of pieces of evidence supporting the variant across all samples"> | |
| 16 ##INFO=<ID=PE,Number=.,Type=Integer,Description="Number of paired-end reads supporting the variant across all samples"> | |
| 17 ##INFO=<ID=SR,Number=.,Type=Integer,Description="Number of split reads supporting the variant across all samples"> | |
| 18 ##INFO=<ID=BD,Number=.,Type=Integer,Description="Amount of BED evidence supporting the variant across all samples"> | |
| 19 ##INFO=<ID=EV,Number=.,Type=String,Description="Type of LUMPY evidence contributing to the variant call"> | |
| 20 ##INFO=<ID=PRPOS,Number=.,Type=String,Description="LUMPY probability curve of the POS breakend"> | |
| 21 ##INFO=<ID=PREND,Number=.,Type=String,Description="LUMPY probability curve of the END breakend"> | |
| 22 ##ALT=<ID=DEL,Description="Deletion"> | |
| 23 ##ALT=<ID=DUP,Description="Duplication"> | |
| 24 ##ALT=<ID=INV,Description="Inversion"> | |
| 25 ##ALT=<ID=DUP:TANDEM,Description="Tandem duplication"> | |
| 26 ##ALT=<ID=INS,Description="Insertion of novel sequence"> | |
| 27 ##ALT=<ID=CNV,Description="Copy number variable region"> | |
| 28 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> | |
| 29 ##FORMAT=<ID=SU,Number=1,Type=Integer,Description="Number of pieces of evidence supporting the variant"> | |
| 30 ##FORMAT=<ID=PE,Number=1,Type=Integer,Description="Number of paired-end reads supporting the variant"> | |
| 31 ##FORMAT=<ID=SR,Number=1,Type=Integer,Description="Number of split reads supporting the variant"> | |
| 32 ##FORMAT=<ID=BD,Number=1,Type=Integer,Description="Amount of BED evidence supporting the variant"> | |
| 33 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sr_input_bam | |
| 34 hg38_gold_U07000.1 14 1_1 N [hg38_gold_U07000.1:1876[N . . SVTYPE=BND;STRANDS=--:19;EVENT=1;MATEID=1_2;CIPOS=0,0;CIEND=0,2;CIPOS95=0,0;CIEND95=0,0;SU=19;SR=19 GT:SU:SR ./.:19:19 | |
| 35 hg38_gold_U07000.1 1876 1_2 N [hg38_gold_U07000.1:14[N . . SVTYPE=BND;STRANDS=--:19;SECONDARY;EVENT=1;MATEID=1_1;CIPOS=0,2;CIEND=0,0;CIPOS95=0,0;CIEND95=0,0;SU=19;SR=19 GT:SU:SR ./.:19:19 | |
| 36 hg38_gold_U07000.1 10 2_1 N [hg38_gold_U07000.1:1897[N . . SVTYPE=BND;STRANDS=--:19;EVENT=2;MATEID=2_2;CIPOS=-1,0;CIEND=-7,5;CIPOS95=0,1;CIEND95=-2,1;IMPRECISE;SU=19;SR=19 GT:SU:SR ./.:19:19 | |
| 37 hg38_gold_U07000.1 1897 2_2 N [hg38_gold_U07000.1:10[N . . SVTYPE=BND;STRANDS=--:19;SECONDARY;EVENT=2;MATEID=2_1;CIPOS=-7,5;CIEND=-1,0;CIPOS95=-2,1;CIEND95=0,1;IMPRECISE;SU=19;SR=19 GT:SU:SR ./.:19:19 |