fritzsedlazeck
commented
4 years ago I dont think that his an issue for SURVIVOR. It will include a header, but the VCF might not be 100% standard conform as important information about the genome and sample name might be missing. Thanks Fritz
One of the CNV detection programs (CNVnator) output contained one line header in vcf and the file parser cannot open the file. My SV file has only duplications which are sorter by the position. Is there any way SURVIVOR can deal with that? Example of my input from CNVnator: TYPE COORDINATE SIZE NormalizedRD P-val1 P-val2 COL1 COL2 COL3
DUP chr1:1635001-1752000 117000 1.41886 4.04724e-08 411000 1.62956e-07 478140 0.259348
DUP chr1:83136001-83490000 354000 1.82362 0 939.166 0 1021.84 0.457598
DUP chr1:116583001-116660000 77000 1.4884 9.03539e-07 861917 2.98472e-06 1.06405e+06 0.223039
DUP chr1:161512001-161678000 166000 1.73613 0 11062.7 0 12855.6 0.440492
DUP chr1:192290001-192386000 96000 1.36988 1.40822e-06 6377.13 5.26661e-06 8363.82 0.00941176
DUP chr1:234776001-234820000 44000 4.1361 0 2.31504 0 5.9965 0.491603
DUP chr2:108650001-108732000 82000 1.73223 0.00025393 8.51826e+06 0.000836588 9.81752e+06 0.389333
DUP chr2:111251001-111994000 743000 1.838 0 68.3844 0 71.693 0.443333
DUP chr2:116148001-116314000 166000 1.30335 1.19691e-05 19704.4 3.14383e-05 22739.1 0.0325521
DUP chr2:231576001-231646000 70000 1.31706 0.0316835 111187 0.0699279 148631 0.0720721
DUP chr3:75360001-75830000 470000 2.00096 0 43241.3 0 45333.5 0.379752
DUP chr3:129999001-130203000 204000 1.61608 0 2.31751e+07 0 2.42964e+07 0.34366
DUP chr3:176010001-176088000 78000 1.3955 3.4452e-05 2.25294e+06 0.000100499 2.70627e+06 0.127688
DUP chr4:3889001-4189000 300000 1.54285 0 6560.45 0 7153.87 0.277279
Thanks