Mercurial > repos > artbio > lumpy_smoove
comparison test-data/result-2.vcf @ 0:ee8fc44b1655 draft
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
| author | artbio |
|---|---|
| date | Tue, 25 Aug 2020 11:35:02 -0400 |
| parents | |
| children | 65b400409455 |
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| -1:000000000000 | 0:ee8fc44b1655 |
|---|---|
| 1 ##fileformat=VCFv4.2 | |
| 2 ##contig=<ID=chrI,length=15072434> | |
| 3 ##smoove_version=0.2.5 | |
| 4 ##reference=reference.fa | |
| 5 ##smoove_count_stats=tumor:2531,2421,156,296 | |
| 6 ##smoove_count_stats=normal:2869,2691,202,330 | |
| 7 ##source=LUMPY | |
| 8 ##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant"> | |
| 9 ##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles"> | |
| 10 ##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record"> | |
| 11 ##INFO=<ID=STRANDS,Number=.,Type=String,Description="Strand orientation of the adjacency in BEDPE format (DEL:+-, DUP:-+, INV:++/--)"> | |
| 12 ##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation"> | |
| 13 ##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS for imprecise variants"> | |
| 14 ##INFO=<ID=CIEND,Number=2,Type=Integer,Description="Confidence interval around END for imprecise variants"> | |
| 15 ##INFO=<ID=CIPOS95,Number=2,Type=Integer,Description="Confidence interval (95%) around POS for imprecise variants"> | |
| 16 ##INFO=<ID=CIEND95,Number=2,Type=Integer,Description="Confidence interval (95%) around END for imprecise variants"> | |
| 17 ##INFO=<ID=MATEID,Number=.,Type=String,Description="ID of mate breakends"> | |
| 18 ##INFO=<ID=EVENT,Number=1,Type=String,Description="ID of event associated to breakend"> | |
| 19 ##INFO=<ID=SECONDARY,Number=0,Type=Flag,Description="Secondary breakend in a multi-line variants"> | |
| 20 ##INFO=<ID=SU,Number=.,Type=Integer,Description="Number of pieces of evidence supporting the variant across all samples"> | |
| 21 ##INFO=<ID=PE,Number=.,Type=Integer,Description="Number of paired-end reads supporting the variant across all samples"> | |
| 22 ##INFO=<ID=SR,Number=.,Type=Integer,Description="Number of split reads supporting the variant across all samples"> | |
| 23 ##INFO=<ID=BD,Number=.,Type=Integer,Description="Amount of BED evidence supporting the variant across all samples"> | |
| 24 ##INFO=<ID=EV,Number=.,Type=String,Description="Type of LUMPY evidence contributing to the variant call"> | |
| 25 ##INFO=<ID=PRPOS,Number=.,Type=String,Description="LUMPY probability curve of the POS breakend"> | |
| 26 ##INFO=<ID=PREND,Number=.,Type=String,Description="LUMPY probability curve of the END breakend"> | |
| 27 ##ALT=<ID=DEL,Description="Deletion"> | |
| 28 ##ALT=<ID=DUP,Description="Duplication"> | |
| 29 ##ALT=<ID=INV,Description="Inversion"> | |
| 30 ##ALT=<ID=DUP:TANDEM,Description="Tandem duplication"> | |
| 31 ##ALT=<ID=INS,Description="Insertion of novel sequence"> | |
| 32 ##ALT=<ID=CNV,Description="Copy number variable region"> | |
| 33 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> | |
| 34 ##FORMAT=<ID=SU,Number=1,Type=Integer,Description="Number of pieces of evidence supporting the variant"> | |
| 35 ##FORMAT=<ID=PE,Number=1,Type=Integer,Description="Number of paired-end reads supporting the variant"> | |
| 36 ##FORMAT=<ID=SR,Number=1,Type=Integer,Description="Number of split reads supporting the variant"> | |
| 37 ##FORMAT=<ID=BD,Number=1,Type=Integer,Description="Amount of BED evidence supporting the variant"> | |
| 38 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT normal tumor | |
| 39 chrI 10416569 1 N <DUP> . . SVTYPE=DUP;STRANDS=-+:4;SVLEN=981;END=10417550;CIPOS=-769,29;CIEND=-30,636;CIPOS95=-165,8;CIEND95=-9,128;IMPRECISE;SU=4;PE=4;SR=0 GT:SU:PE:SR ./.:4:4:0 ./.:0:0:0 |