Mercurial > repos > artbio > lumpy_smoove
diff test-data/result-3.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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/result-3.vcf Tue Aug 25 11:35:02 2020 -0400 @@ -0,0 +1,39 @@ +##fileformat=VCFv4.2 +##contig=<ID=chrI,length=15072434> +##smoove_version=0.2.5 +##reference=reference.fa +##smoove_count_stats=tumor:2869,2691,202,330 +##smoove_count_stats=normal:2531,2421,156,296 +##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 normal tumor +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 ./.:0:0:0 ./.:4:4:0