Mercurial > repos > artbio > lumpy_sv
annotate test-data/output_two.paired_end.vcf @ 6:48e97429a749 draft default tip
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_sv commit 37c0f0938a5cad74c954a89827a6a08bbbb81cb0
| author | artbio |
|---|---|
| date | Mon, 08 Jul 2024 22:23:10 +0000 |
| parents | da5aae7550b3 |
| children |
| rev | line source |
|---|---|
|
3
da5aae7550b3
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy-sv commit 810390d1104d08df5cf35d501b50650455b99684"
artbio
parents:
diff
changeset
|
1 ##fileformat=VCFv4.2 |
|
da5aae7550b3
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy-sv commit 810390d1104d08df5cf35d501b50650455b99684"
artbio
parents:
diff
changeset
|
2 ##source=LUMPY |
|
da5aae7550b3
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy-sv commit 810390d1104d08df5cf35d501b50650455b99684"
artbio
parents:
diff
changeset
|
3 ##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant"> |
|
da5aae7550b3
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy-sv commit 810390d1104d08df5cf35d501b50650455b99684"
artbio
parents:
diff
changeset
|
4 ##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles"> |
|
da5aae7550b3
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy-sv commit 810390d1104d08df5cf35d501b50650455b99684"
artbio
parents:
diff
changeset
|
5 ##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record"> |
|
da5aae7550b3
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy-sv commit 810390d1104d08df5cf35d501b50650455b99684"
artbio
parents:
diff
changeset
|
6 ##INFO=<ID=STRANDS,Number=.,Type=String,Description="Strand orientation of the adjacency in BEDPE format (DEL:+-, DUP:-+, INV:++/--)"> |
|
da5aae7550b3
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy-sv commit 810390d1104d08df5cf35d501b50650455b99684"
artbio
parents:
diff
changeset
|
7 ##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation"> |
|
da5aae7550b3
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy-sv commit 810390d1104d08df5cf35d501b50650455b99684"
artbio
parents:
diff
changeset
|
8 ##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS for imprecise variants"> |
|
da5aae7550b3
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy-sv commit 810390d1104d08df5cf35d501b50650455b99684"
artbio
parents:
diff
changeset
|
9 ##INFO=<ID=CIEND,Number=2,Type=Integer,Description="Confidence interval around END for imprecise variants"> |
|
da5aae7550b3
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy-sv commit 810390d1104d08df5cf35d501b50650455b99684"
artbio
parents:
diff
changeset
|
10 ##INFO=<ID=CIPOS95,Number=2,Type=Integer,Description="Confidence interval (95%) around POS for imprecise variants"> |
|
da5aae7550b3
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy-sv commit 810390d1104d08df5cf35d501b50650455b99684"
artbio
parents:
diff
changeset
|
11 ##INFO=<ID=CIEND95,Number=2,Type=Integer,Description="Confidence interval (95%) around END for imprecise variants"> |
|
da5aae7550b3
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy-sv commit 810390d1104d08df5cf35d501b50650455b99684"
artbio
parents:
diff
changeset
|
12 ##INFO=<ID=MATEID,Number=.,Type=String,Description="ID of mate breakends"> |
|
da5aae7550b3
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy-sv commit 810390d1104d08df5cf35d501b50650455b99684"
artbio
parents:
diff
changeset
|
13 ##INFO=<ID=EVENT,Number=1,Type=String,Description="ID of event associated to breakend"> |
|
da5aae7550b3
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy-sv commit 810390d1104d08df5cf35d501b50650455b99684"
artbio
parents:
diff
changeset
|
14 ##INFO=<ID=SECONDARY,Number=0,Type=Flag,Description="Secondary breakend in a multi-line variants"> |
|
da5aae7550b3
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy-sv commit 810390d1104d08df5cf35d501b50650455b99684"
artbio
parents:
diff
changeset
|
15 ##INFO=<ID=SU,Number=.,Type=Integer,Description="Number of pieces of evidence supporting the variant across all samples"> |
|
da5aae7550b3
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy-sv commit 810390d1104d08df5cf35d501b50650455b99684"
artbio
parents:
diff
changeset
|
16 ##INFO=<ID=PE,Number=.,Type=Integer,Description="Number of paired-end reads supporting the variant across all samples"> |
|
da5aae7550b3
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy-sv commit 810390d1104d08df5cf35d501b50650455b99684"
artbio
parents:
diff
changeset
|
17 ##INFO=<ID=SR,Number=.,Type=Integer,Description="Number of split reads supporting the variant across all samples"> |
|
da5aae7550b3
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy-sv commit 810390d1104d08df5cf35d501b50650455b99684"
artbio
parents:
diff
changeset
|
18 ##INFO=<ID=BD,Number=.,Type=Integer,Description="Amount of BED evidence supporting the variant across all samples"> |
|
da5aae7550b3
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy-sv commit 810390d1104d08df5cf35d501b50650455b99684"
artbio
parents:
diff
changeset
|
19 ##INFO=<ID=EV,Number=.,Type=String,Description="Type of LUMPY evidence contributing to the variant call"> |
|
da5aae7550b3
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy-sv commit 810390d1104d08df5cf35d501b50650455b99684"
artbio
parents:
diff
changeset
|
20 ##INFO=<ID=PRPOS,Number=.,Type=String,Description="LUMPY probability curve of the POS breakend"> |
|
da5aae7550b3
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy-sv commit 810390d1104d08df5cf35d501b50650455b99684"
artbio
parents:
diff
changeset
|
21 ##INFO=<ID=PREND,Number=.,Type=String,Description="LUMPY probability curve of the END breakend"> |
|
da5aae7550b3
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy-sv commit 810390d1104d08df5cf35d501b50650455b99684"
artbio
parents:
diff
changeset
|
22 ##ALT=<ID=DEL,Description="Deletion"> |
|
da5aae7550b3
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy-sv commit 810390d1104d08df5cf35d501b50650455b99684"
artbio
parents:
diff
changeset
|
23 ##ALT=<ID=DUP,Description="Duplication"> |
|
da5aae7550b3
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy-sv commit 810390d1104d08df5cf35d501b50650455b99684"
artbio
parents:
diff
changeset
|
24 ##ALT=<ID=INV,Description="Inversion"> |
|
da5aae7550b3
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy-sv commit 810390d1104d08df5cf35d501b50650455b99684"
artbio
parents:
diff
changeset
|
25 ##ALT=<ID=DUP:TANDEM,Description="Tandem duplication"> |
|
da5aae7550b3
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy-sv commit 810390d1104d08df5cf35d501b50650455b99684"
artbio
parents:
diff
changeset
|
26 ##ALT=<ID=INS,Description="Insertion of novel sequence"> |
|
da5aae7550b3
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy-sv commit 810390d1104d08df5cf35d501b50650455b99684"
artbio
parents:
diff
changeset
|
27 ##ALT=<ID=CNV,Description="Copy number variable region"> |
|
da5aae7550b3
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy-sv commit 810390d1104d08df5cf35d501b50650455b99684"
artbio
parents:
diff
changeset
|
28 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> |
|
da5aae7550b3
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy-sv commit 810390d1104d08df5cf35d501b50650455b99684"
artbio
parents:
diff
changeset
|
29 ##FORMAT=<ID=SU,Number=1,Type=Integer,Description="Number of pieces of evidence supporting the variant"> |
|
da5aae7550b3
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy-sv commit 810390d1104d08df5cf35d501b50650455b99684"
artbio
parents:
diff
changeset
|
30 ##FORMAT=<ID=PE,Number=1,Type=Integer,Description="Number of paired-end reads supporting the variant"> |
|
da5aae7550b3
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy-sv commit 810390d1104d08df5cf35d501b50650455b99684"
artbio
parents:
diff
changeset
|
31 ##FORMAT=<ID=SR,Number=1,Type=Integer,Description="Number of split reads supporting the variant"> |
|
da5aae7550b3
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy-sv commit 810390d1104d08df5cf35d501b50650455b99684"
artbio
parents:
diff
changeset
|
32 ##FORMAT=<ID=BD,Number=1,Type=Integer,Description="Amount of BED evidence supporting the variant"> |
|
da5aae7550b3
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy-sv commit 810390d1104d08df5cf35d501b50650455b99684"
artbio
parents:
diff
changeset
|
33 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT inputA.bam inputB.bam |
|
da5aae7550b3
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy-sv commit 810390d1104d08df5cf35d501b50650455b99684"
artbio
parents:
diff
changeset
|
34 22 23289741 1_1 N N[9:130703751[ . . SVTYPE=BND;STRANDS=+-:8;EVENT=1;MATEID=1_2;CIPOS=-5,4;CIEND=-5,9;CIPOS95=0,0;CIEND95=0,0;SU=8;PE=1;SR=7;PRPOS=2.51045e-16,3.97879e-13,6.30596e-10,9.99428e-07,0.00158399,0.996836,0.00157659,2.48311e-06,3.9272e-09,6.20457e-12;PREND=9.46531e-15,5.9925e-12,3.81943e-09,2.43414e-06,0.00154348,0.988348,0.0100041,0.000100524,1.00845e-06,1.0173e-08,1.03097e-10,1.648e-13,2.63008e-16,4.19721e-19,6.68765e-22 GT:SU:PE:SR ./.:8:1:7 ./.:0:0:0 |
|
da5aae7550b3
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy-sv commit 810390d1104d08df5cf35d501b50650455b99684"
artbio
parents:
diff
changeset
|
35 9 130703751 1_2 N ]22:23289741]N . . SVTYPE=BND;STRANDS=-+:8;SECONDARY;EVENT=1;MATEID=1_1;CIPOS=-5,9;CIEND=-5,4;CIPOS95=0,0;CIEND95=0,0;SU=8;PE=1;SR=7;PRPOS=9.46531e-15,5.9925e-12,3.81943e-09,2.43414e-06,0.00154348,0.988348,0.0100041,0.000100524,1.00845e-06,1.0173e-08,1.03097e-10,1.648e-13,2.63008e-16,4.19721e-19,6.68765e-22;PREND=2.51045e-16,3.97879e-13,6.30596e-10,9.99428e-07,0.00158399,0.996836,0.00157659,2.48311e-06,3.9272e-09,6.20457e-12 GT:SU:PE:SR ./.:8:1:7 ./.:0:0:0 |
|
da5aae7550b3
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy-sv commit 810390d1104d08df5cf35d501b50650455b99684"
artbio
parents:
diff
changeset
|
36 22 23289769 2_1 N ]9:130703785]N . . SVTYPE=BND;STRANDS=-+:6;EVENT=2;MATEID=2_2;CIPOS=-10,9;CIEND=-8,6;CIPOS95=0,0;CIEND95=0,0;SU=6;PE=1;SR=5;PRPOS=9.56458e-21,9.57993e-19,9.63619e-17,9.66176e-15,9.68222e-13,9.70268e-11,9.73337e-09,9.75383e-07,9.8152e-05,0.00983566,0.986124,0.00392583,1.5629e-05,6.22202e-08,2.47703e-10,9.86124e-13,3.92583e-15,1.5629e-17,6.22202e-20,2.47703e-22;PREND=1.04138e-16,1.03354e-14,1.02805e-12,1.02099e-10,1.01393e-08,1.00531e-06,9.91976e-05,0.00983351,0.980214,0.00975509,9.63746e-05,9.49631e-07,9.44926e-09,9.35516e-11,9.26106e-13 GT:SU:PE:SR ./.:6:1:5 ./.:0:0:0 |
|
da5aae7550b3
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy-sv commit 810390d1104d08df5cf35d501b50650455b99684"
artbio
parents:
diff
changeset
|
37 9 130703785 2_2 N N[22:23289769[ . . SVTYPE=BND;STRANDS=+-:6;SECONDARY;EVENT=2;MATEID=2_1;CIPOS=-8,6;CIEND=-10,9;CIPOS95=0,0;CIEND95=0,0;SU=6;PE=1;SR=5;PRPOS=1.04138e-16,1.03354e-14,1.02805e-12,1.02099e-10,1.01393e-08,1.00531e-06,9.91976e-05,0.00983351,0.980214,0.00975509,9.63746e-05,9.49631e-07,9.44926e-09,9.35516e-11,9.26106e-13;PREND=9.56458e-21,9.57993e-19,9.63619e-17,9.66176e-15,9.68222e-13,9.70268e-11,9.73337e-09,9.75383e-07,9.8152e-05,0.00983566,0.986124,0.00392583,1.5629e-05,6.22202e-08,2.47703e-10,9.86124e-13,3.92583e-15,1.5629e-17,6.22202e-20,2.47703e-22 GT:SU:PE:SR ./.:6:1:5 ./.:0:0:0 |
|
da5aae7550b3
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy-sv commit 810390d1104d08df5cf35d501b50650455b99684"
artbio
parents:
diff
changeset
|
38 22 23292033 3_1 N ]9:130783718]N . . SVTYPE=BND;STRANDS=-+:4;EVENT=3;MATEID=3_2;CIPOS=-10,9;CIEND=-10,9;CIPOS95=-1,1;CIEND95=-1,1;IMPRECISE;SU=4;PE=1;SR=3;PRPOS=8.23016e-13,1.31329e-11,2.09771e-10,3.347e-09,5.34553e-08,8.53258e-07,1.36259e-05,0.000217259,0.00346568,0.0551999,0.88134,0.0559631,0.00355855,0.00022594,1.4338e-05,9.08558e-07,5.7626e-08,3.65831e-09,9.18926e-11,2.30824e-12;PREND=9.82279e-13,1.54152e-11,2.41893e-10,3.77889e-09,5.93699e-08,9.25795e-07,1.45855e-05,0.000228742,0.00360339,0.0562406,0.881709,0.054589,0.00338949,0.000210056,1.31444e-05,8.21092e-07,5.1112e-08,3.18107e-09,1.97944e-10,1.23366e-11 GT:SU:PE:SR ./.:0:0:0 ./.:4:1:3 |
|
da5aae7550b3
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy-sv commit 810390d1104d08df5cf35d501b50650455b99684"
artbio
parents:
diff
changeset
|
39 9 130783718 3_2 N N[22:23292033[ . . SVTYPE=BND;STRANDS=+-:4;SECONDARY;EVENT=3;MATEID=3_1;CIPOS=-10,9;CIEND=-10,9;CIPOS95=-1,1;CIEND95=-1,1;IMPRECISE;SU=4;PE=1;SR=3;PRPOS=9.82279e-13,1.54152e-11,2.41893e-10,3.77889e-09,5.93699e-08,9.25795e-07,1.45855e-05,0.000228742,0.00360339,0.0562406,0.881709,0.054589,0.00338949,0.000210056,1.31444e-05,8.21092e-07,5.1112e-08,3.18107e-09,1.97944e-10,1.23366e-11;PREND=8.23016e-13,1.31329e-11,2.09771e-10,3.347e-09,5.34553e-08,8.53258e-07,1.36259e-05,0.000217259,0.00346568,0.0551999,0.88134,0.0559631,0.00355855,0.00022594,1.4338e-05,9.08558e-07,5.7626e-08,3.65831e-09,9.18926e-11,2.30824e-12 GT:SU:PE:SR ./.:0:0:0 ./.:4:1:3 |