Mercurial > repos > iuc > cnv_vcf2json
diff test-data/input.vcf @ 1:6763389420f5 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-vcf2json commit fc1282ec68b346988203ead860e9b9d6a47e9efb
| author | iuc |
|---|---|
| date | Sat, 01 Mar 2025 11:47:41 +0000 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input.vcf Sat Mar 01 11:47:41 2025 +0000 @@ -0,0 +1,72 @@ +##fileformat=VCFv4.2 +##fileDate=20250206 +##source=CNVkit v0.9.12 +##INFO=<ID=CIEND,Number=2,Type=Integer,Description="Confidence interval around END for imprecise variants"> +##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS for imprecise variants"> +##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record"> +##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation"> +##INFO=<ID=SVLEN,Number=1,Type=Integer,Description="Difference in length between REF and ALT alleles"> +##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant"> +##INFO=<ID=FOLD_CHANGE,Number=1,Type=Float,Description="Fold change"> +##INFO=<ID=FOLD_CHANGE_LOG,Number=1,Type=Float,Description="Log fold change"> +##INFO=<ID=PROBES,Number=1,Type=Integer,Description="Number of probes in CNV"> +##ALT=<ID=DEL,Description="Deletion"> +##ALT=<ID=DUP,Description="Duplication"> +##ALT=<ID=CNV,Description="Copy number variable region"> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype quality"> +##FORMAT=<ID=CN,Number=1,Type=Integer,Description="Copy number genotype for imprecise events"> +##FORMAT=<ID=CNQ,Number=1,Type=Float,Description="Copy number genotype quality for imprecise events"> +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SampleID +chr17 63642 . N <DEL> . . IMPRECISE;SVTYPE=DEL;END=169340;SVLEN=-105698;FOLD_CHANGE=0.7464704212057787;FOLD_CHANGE_LOG=-0.421843;PROBES=5 GT:GQ 0/1:5 +chr17 171062 . N <DEL> . . IMPRECISE;SVTYPE=DEL;END=975994;SVLEN=-804932;FOLD_CHANGE=0.959723882595653;FOLD_CHANGE_LOG=-0.0593087;PROBES=76 GT:GQ 0/1:76 +chr17 976864 . N <DEL> . . IMPRECISE;SVTYPE=DEL;END=995090;SVLEN=-18226;FOLD_CHANGE=0.7835471517981237;FOLD_CHANGE_LOG=-0.351908;PROBES=5 GT:GQ 0/1:5 +chr17 1003876 . N <DEL> . . IMPRECISE;SVTYPE=DEL;END=1370635;SVLEN=-366759;FOLD_CHANGE=0.9559443899390699;FOLD_CHANGE_LOG=-0.0650014;PROBES=17 GT:GQ 0/1:17 +chr17 1370773 . N <DEL> . . IMPRECISE;SVTYPE=DEL;END=1371602;SVLEN=-829;FOLD_CHANGE=0.6795511253930977;FOLD_CHANGE_LOG=-0.557346;PROBES=4 GT:GQ 0/1:4 +chr17 1371696 . N <DEL> . . IMPRECISE;SVTYPE=DEL;END=7077386;SVLEN=-5705690;FOLD_CHANGE=0.9831802905897856;FOLD_CHANGE_LOG=-0.0244721;PROBES=1185 GT:GQ 0/1:1185 +chr17 7077456 . N <DEL> . . IMPRECISE;SVTYPE=DEL;END=7081882;SVLEN=-4426;FOLD_CHANGE=0.7017421863290814;FOLD_CHANGE_LOG=-0.510987;PROBES=6 GT:GQ 0/1:6 +chr17 7094026 . N <DEL> . . IMPRECISE;SVTYPE=DEL;END=15457143;SVLEN=-8363117;FOLD_CHANGE=0.9753768930200515;FOLD_CHANGE_LOG=-0.0359683;PROBES=1358 GT:GQ 0/1:1358 +chr17 15458595 . N <DEL> . . IMPRECISE;SVTYPE=DEL;END=15472344;SVLEN=-13749;FOLD_CHANGE=0.7204913424795425;FOLD_CHANGE_LOG=-0.472947;PROBES=3 GT:GQ 0/1:3 +chr17 15492288 . N <DEL> . . IMPRECISE;SVTYPE=DEL;END=15510997;SVLEN=-18709;FOLD_CHANGE=0.94346617461336;FOLD_CHANGE_LOG=-0.0839573;PROBES=7 GT:GQ 0/1:7 +chr17 15516014 . N <DEL> . . IMPRECISE;SVTYPE=DEL;END=15640837;SVLEN=-124823;FOLD_CHANGE=0.7449027533881352;FOLD_CHANGE_LOG=-0.424876;PROBES=22 GT:GQ 0/1:22 +chr17 15641310 . N <DEL> . . IMPRECISE;SVTYPE=DEL;END=16553058;SVLEN=-911748;FOLD_CHANGE=1.0300478798864319;FOLD_CHANGE_LOG=0.0427114;PROBES=104 GT:GQ 0/1:104 +chr17 16593714 . N <DEL> . . IMPRECISE;SVTYPE=DEL;END=16638957;SVLEN=-45243;FOLD_CHANGE=0.5908709597957374;FOLD_CHANGE_LOG=-0.759085;PROBES=12 GT:GQ 0/1:12 +chr17 16664738 . N <DUP> . . IMPRECISE;SVTYPE=DUP;END=16676023;SVLEN=11285;FOLD_CHANGE=1.2389448764191389;FOLD_CHANGE_LOG=0.309112;PROBES=5 GT:GQ:CN:CNQ 0/1:0:3:5 +chr17 16676810 . N <DEL> . . IMPRECISE;SVTYPE=DEL;END=17717724;SVLEN=-1040914;FOLD_CHANGE=1.0099897838199476;FOLD_CHANGE_LOG=0.0143407;PROBES=77 GT:GQ 0/1:77 +chr17 17717928 . N <DUP> . . IMPRECISE;SVTYPE=DUP;END=17718258;SVLEN=330;FOLD_CHANGE=1.2614622207412653;FOLD_CHANGE_LOG=0.335097;PROBES=2 GT:GQ:CN:CNQ 0/1:0:3:2 +chr17 17718534 . N <DEL> . . IMPRECISE;SVTYPE=DEL;END=17720032;SVLEN=-1498;FOLD_CHANGE=0.8080805421320396;FOLD_CHANGE_LOG=-0.307429;PROBES=4 GT:GQ 0/1:4 +chr17 17720271 . N <DEL> . . IMPRECISE;SVTYPE=DEL;END=18286901;SVLEN=-566630;FOLD_CHANGE=1.0054791111957748;FOLD_CHANGE_LOG=0.00788311;PROBES=225 GT:GQ 0/1:225 +chr17 18291532 . N <DEL> . . IMPRECISE;SVTYPE=DEL;END=18631071;SVLEN=-339539;FOLD_CHANGE=0.6628466290375354;FOLD_CHANGE_LOG=-0.593253;PROBES=27 GT:GQ 0/1:27 +chr17 18634382 . N <DEL> . . IMPRECISE;SVTYPE=DEL;END=18925457;SVLEN=-291075;FOLD_CHANGE=0.9647550528950727;FOLD_CHANGE_LOG=-0.0517654;PROBES=59 GT:GQ 0/1:59 +chr17 18927527 . N <DEL> . . IMPRECISE;SVTYPE=DEL;END=19187027;SVLEN=-259500;FOLD_CHANGE=0.5791757084985782;FOLD_CHANGE_LOG=-0.787927;PROBES=4 GT:GQ 0/1:4 +chr17 19213197 . N <DEL> . . IMPRECISE;SVTYPE=DEL;END=19290431;SVLEN=-77234;FOLD_CHANGE=1.0153379493336925;FOLD_CHANGE_LOG=0.02196;PROBES=28 GT:GQ 0/1:28 +chr17 19290462 . N <DEL> . . IMPRECISE;SVTYPE=DEL;END=19314775;SVLEN=-24313;FOLD_CHANGE=0.7125257214335718;FOLD_CHANGE_LOG=-0.488986;PROBES=2 GT:GQ 0/1:2 +chr17 19314942 . N <DEL> . . IMPRECISE;SVTYPE=DEL;END=20209395;SVLEN=-894453;FOLD_CHANGE=1.0129824643579048;FOLD_CHANGE_LOG=0.0186092;PROBES=122 GT:GQ 0/1:122 +chr17 20217288 . N <DEL> . . IMPRECISE;SVTYPE=DEL;END=20363756;SVLEN=-146468;FOLD_CHANGE=0.2056196432884299;FOLD_CHANGE_LOG=-2.28195;PROBES=10 GT:GQ 1/1:10 +chr17 20370744 . N <DEL> . . IMPRECISE;SVTYPE=DEL;END=22023462;SVLEN=-1652718;FOLD_CHANGE=0.9869532815807457;FOLD_CHANGE_LOG=-0.0189463;PROBES=40 GT:GQ 0/1:40 +chr17 25621421 . N <DEL> . . IMPRECISE;SVTYPE=DEL;END=34432035;SVLEN=-8810614;FOLD_CHANGE=1.0063912542057964;FOLD_CHANGE_LOG=0.00919129;PROBES=1168 GT:GQ 0/1:1168 +chr17 34432617 . N <DEL> . . IMPRECISE;SVTYPE=DEL;END=34848743;SVLEN=-416126;FOLD_CHANGE=0.08615987696725817;FOLD_CHANGE_LOG=-3.53684;PROBES=26 GT:GQ 1/1:26 +chr17 34849769 . N <DEL> . . IMPRECISE;SVTYPE=DEL;END=36099630;SVLEN=-1249861;FOLD_CHANGE=1.0166420433824157;FOLD_CHANGE_LOG=0.0238118;PROBES=193 GT:GQ 0/1:193 +chr17 36104531 . N <DEL> . . IMPRECISE;SVTYPE=DEL;END=36454592;SVLEN=-350061;FOLD_CHANGE=0.28542230754373005;FOLD_CHANGE_LOG=-1.80883;PROBES=14 GT:GQ 1/1:14 +chr17 36455316 . N <DEL> . . IMPRECISE;SVTYPE=DEL;END=39406437;SVLEN=-2951121;FOLD_CHANGE=0.9948720373067039;FOLD_CHANGE_LOG=-0.00741712;PROBES=661 GT:GQ 0/1:661 +chr17 39411637 . N <DEL> . . IMPRECISE;SVTYPE=DEL;END=39459103;SVLEN=-47466;FOLD_CHANGE=0.683827809625486;FOLD_CHANGE_LOG=-0.548295;PROBES=4 GT:GQ 0/1:4 +chr17 39463951 . N <DEL> . . IMPRECISE;SVTYPE=DEL;END=40369482;SVLEN=-905531;FOLD_CHANGE=0.9873504837918345;FOLD_CHANGE_LOG=-0.0183658;PROBES=323 GT:GQ 0/1:323 +chr17 40370168 . N <DEL> . . IMPRECISE;SVTYPE=DEL;END=40371860;SVLEN=-1692;FOLD_CHANGE=0.7057210754625698;FOLD_CHANGE_LOG=-0.50283;PROBES=4 GT:GQ 0/1:4 +chr17 40375399 . N <DEL> . . IMPRECISE;SVTYPE=DEL;END=40447811;SVLEN=-72412;FOLD_CHANGE=1.1111980710252125;FOLD_CHANGE_LOG=0.152116;PROBES=8 GT:GQ 0/1:8 +chr17 40451768 . N <DEL> . . IMPRECISE;SVTYPE=DEL;END=40452888;SVLEN=-1120;FOLD_CHANGE=0.6524381281566785;FOLD_CHANGE_LOG=-0.616087;PROBES=3 GT:GQ 0/1:3 +chr17 40453292 . N <DEL> . . IMPRECISE;SVTYPE=DEL;END=44145033;SVLEN=-3691741;FOLD_CHANGE=0.9970208844681734;FOLD_CHANGE_LOG=-0.00430437;PROBES=916 GT:GQ 0/1:916 +chr17 44159806 . N <DUP> . . IMPRECISE;SVTYPE=DUP;END=44172067;SVLEN=12261;FOLD_CHANGE=1.428500954243693;FOLD_CHANGE_LOG=0.514502;PROBES=2 GT:GQ:CN:CNQ 0/1:0:3:2 +chr17 44248220 . N <DEL> . . IMPRECISE;SVTYPE=DEL;END=44788485;SVLEN=-540265;FOLD_CHANGE=0.24905391591000614;FOLD_CHANGE_LOG=-2.00547;PROBES=29 GT:GQ 1/1:29 +chr17 44791218 . N <DEL> . . IMPRECISE;SVTYPE=DEL;END=45016126;SVLEN=-224908;FOLD_CHANGE=1.0038784515470944;FOLD_CHANGE_LOG=0.0055846;PROBES=21 GT:GQ 0/1:21 +chr17 45017920 . N <DEL> . . IMPRECISE;SVTYPE=DEL;END=45137515;SVLEN=-119595;FOLD_CHANGE=0.5868863260265956;FOLD_CHANGE_LOG=-0.768847;PROBES=6 GT:GQ 0/1:6 +chr17 45198300 . N <DEL> . . IMPRECISE;SVTYPE=DEL;END=57650596;SVLEN=-12452296;FOLD_CHANGE=1.0082919287963463;FOLD_CHANGE_LOG=0.0119134;PROBES=1206 GT:GQ 0/1:1206 +chr17 57651100 . N <DEL> . . IMPRECISE;SVTYPE=DEL;END=57676844;SVLEN=-25744;FOLD_CHANGE=0.51403339693734;FOLD_CHANGE_LOG=-0.960066;PROBES=10 GT:GQ 1/1:10 +chr17 57679882 . N <DEL> . . IMPRECISE;SVTYPE=DEL;END=61899528;SVLEN=-4219646;FOLD_CHANGE=1.0130135699005758;FOLD_CHANGE_LOG=0.0186535;PROBES=517 GT:GQ 0/1:517 +chr17 61901176 . N <DEL> . . IMPRECISE;SVTYPE=DEL;END=61901771;SVLEN=-595;FOLD_CHANGE=0.6646574944113218;FOLD_CHANGE_LOG=-0.589317;PROBES=3 GT:GQ 0/1:3 +chr17 61901996 . N <DEL> . . IMPRECISE;SVTYPE=DEL;END=61916041;SVLEN=-14045;FOLD_CHANGE=0.9795525528106097;FOLD_CHANGE_LOG=-0.0298052;PROBES=34 GT:GQ 0/1:34 +chr17 61949485 . N <DEL> . . IMPRECISE;SVTYPE=DEL;END=61950974;SVLEN=-1489;FOLD_CHANGE=0.6435593021910756;FOLD_CHANGE_LOG=-0.635855;PROBES=5 GT:GQ 0/1:5 +chr17 61957592 . N <DEL> . . IMPRECISE;SVTYPE=DEL;END=61959161;SVLEN=-1569;FOLD_CHANGE=0.9555894293342413;FOLD_CHANGE_LOG=-0.0655372;PROBES=4 GT:GQ 0/1:4 +chr17 61972381 . N <DEL> . . IMPRECISE;SVTYPE=DEL;END=61973871;SVLEN=-1490;FOLD_CHANGE=0.5087846322344922;FOLD_CHANGE_LOG=-0.974873;PROBES=5 GT:GQ 1/1:5 +chr17 61987070 . N <DEL> . . IMPRECISE;SVTYPE=DEL;END=79991705;SVLEN=-18004635;FOLD_CHANGE=0.9953613201986847;FOLD_CHANGE_LOG=-0.00670777;PROBES=2428 GT:GQ 0/1:2428 +chr17 79993835 . N <DEL> . . IMPRECISE;SVTYPE=DEL;END=79994519;SVLEN=-684;FOLD_CHANGE=0.7454890153916679;FOLD_CHANGE_LOG=-0.423741;PROBES=4 GT:GQ 0/1:4 +chr17 79994596 . N <DEL> . . IMPRECISE;SVTYPE=DEL;END=81052320;SVLEN=-1057724;FOLD_CHANGE=1.003457350653;FOLD_CHANGE_LOG=0.0049793;PROBES=239 GT:GQ 0/1:239