Mercurial > repos > hepcat72 > lumpyexpress
diff test-data/lumpy-test1.vcf @ 0:e5150e64206a draft
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
| author | hepcat72 |
|---|---|
| date | Tue, 16 Oct 2018 15:55:49 -0400 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/lumpy-test1.vcf Tue Oct 16 15:55:49 2018 -0400 @@ -0,0 +1,36 @@ +##fileformat=VCFv4.2 +##source=LUMPY +##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant"> +##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles"> +##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record"> +##INFO=<ID=STRANDS,Number=.,Type=String,Description="Strand orientation of the adjacency in BEDPE format (DEL:+-, DUP:-+, INV:++/--)"> +##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation"> +##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS for imprecise variants"> +##INFO=<ID=CIEND,Number=2,Type=Integer,Description="Confidence interval around END for imprecise variants"> +##INFO=<ID=CIPOS95,Number=2,Type=Integer,Description="Confidence interval (95%) around POS for imprecise variants"> +##INFO=<ID=CIEND95,Number=2,Type=Integer,Description="Confidence interval (95%) around END for imprecise variants"> +##INFO=<ID=MATEID,Number=.,Type=String,Description="ID of mate breakends"> +##INFO=<ID=EVENT,Number=1,Type=String,Description="ID of event associated to breakend"> +##INFO=<ID=SECONDARY,Number=0,Type=Flag,Description="Secondary breakend in a multi-line variants"> +##INFO=<ID=SU,Number=.,Type=Integer,Description="Number of pieces of evidence supporting the variant across all samples"> +##INFO=<ID=PE,Number=.,Type=Integer,Description="Number of paired-end reads supporting the variant across all samples"> +##INFO=<ID=SR,Number=.,Type=Integer,Description="Number of split reads supporting the variant across all samples"> +##INFO=<ID=BD,Number=.,Type=Integer,Description="Amount of BED evidence supporting the variant across all samples"> +##INFO=<ID=EV,Number=.,Type=String,Description="Type of LUMPY evidence contributing to the variant call"> +##INFO=<ID=PRPOS,Number=.,Type=String,Description="LUMPY probability curve of the POS breakend"> +##INFO=<ID=PREND,Number=.,Type=String,Description="LUMPY probability curve of the END breakend"> +##ALT=<ID=DEL,Description="Deletion"> +##ALT=<ID=DUP,Description="Duplication"> +##ALT=<ID=INV,Description="Inversion"> +##ALT=<ID=DUP:TANDEM,Description="Tandem duplication"> +##ALT=<ID=INS,Description="Insertion of novel sequence"> +##ALT=<ID=CNV,Description="Copy number variable region"> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +##FORMAT=<ID=SU,Number=1,Type=Integer,Description="Number of pieces of evidence supporting the variant"> +##FORMAT=<ID=PE,Number=1,Type=Integer,Description="Number of paired-end reads supporting the variant"> +##FORMAT=<ID=SR,Number=1,Type=Integer,Description="Number of split reads supporting the variant"> +##FORMAT=<ID=BD,Number=1,Type=Integer,Description="Amount of BED evidence supporting the variant"> +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT JSS-Vmut-01__Read JSS-Vmut-12__Read JSS-Vmut-14__Read +NC_009016.1 1417 1_1 N [NC_009016.1:19752[N . . SVTYPE=BND;STRANDS=--:5;EVENT=1;MATEID=1_2;CIPOS=-128,9;CIEND=-291,9;CIPOS95=-92,2;CIEND95=-121,2;IMPRECISE;SU=5;PE=5;SR=0 GT:SU:PE:SR ./.:1:1:0 ./.:4:4:0 ./.:0:0:0 +NC_009016.1 19752 1_2 N [NC_009016.1:1417[N . . SVTYPE=BND;STRANDS=--:5;SECONDARY;EVENT=1;MATEID=1_1;CIPOS=-291,9;CIEND=-128,9;CIPOS95=-121,2;CIEND95=-92,2;IMPRECISE;SU=5;PE=5;SR=0 GT:SU:PE:SR ./.:1:1:0 ./.:4:4:0 ./.:0:0:0 +NC_009016.1 10 2 N <DUP> . . SVTYPE=DUP;STRANDS=-+:350;SVLEN=38187;END=38197;CIPOS=0,0;CIEND=0,0;CIPOS95=0,0;CIEND95=0,0;SU=350;PE=249;SR=101 GT:SU:PE:SR ./.:84:46:38 ./.:162:123:39 ./.:104:80:24