Mercurial > repos > iuc > lumpy_sv
diff test-data/sample.vcf @ 0:477a07f387e0 draft
"planemo upload for repository https://github.com/arq5x/lumpy-sv commit cce17262b21b0964c31eb983bac5e89ae92b8ee9"
| author | iuc |
|---|---|
| date | Thu, 12 Nov 2020 16:48:15 +0000 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sample.vcf Thu Nov 12 16:48:15 2020 +0000 @@ -0,0 +1,35 @@ +##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 sample1 +chr8 245202 1 N <DEL> . . SVTYPE=DEL;STRANDS=+-:3;SVLEN=-229;END=245431;CIPOS=-10,64;CIEND=-51,9;CIPOS95=-1,33;CIEND95=-22,3;IMPRECISE;SU=3;PE=3 GT:SU:PE ./.:3:3 +chr8 246846 2 N <DEL> . . SVTYPE=DEL;STRANDS=+-:2;SVLEN=-176;END=247022;CIPOS=-10,186;CIEND=-159,21;CIPOS95=0,137;CIEND95=-95,13;IMPRECISE;SU=2;PE=2 GT:SU:PE ./.:2:2