Mercurial > repos > plus91-technologies-pvt-ltd > softsearch
comparison 2.4/script/output.vcf @ 13:e3609c8714fb draft
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| author | plus91-technologies-pvt-ltd |
|---|---|
| date | Fri, 30 May 2014 03:37:55 -0400 |
| parents | |
| children |
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| 12:980fce54e60a | 13:e3609c8714fb |
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| 1 ##fileformat=VCFv4.1 | |
| 2 ##fileDate=2014-05-05 12:07:11 | |
| 3 ##source=SoftSearch.pl | |
| 4 ##reference=example.fasta | |
| 5 ##Usage= SoftSearch.pl -l 5 -q 20 -r 5 -d 300 -m 5 -u 0 -s 6 -b Example.bam -f example.fasta -o output.vcf | |
| 6 ##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant"> | |
| 7 ##INFO=<ID=EVENT,Number=1,Type=String,Description="ID of event associated to breakend"> | |
| 8 ##INFO=<ID=MATEID,Number=.,Type=String,Description="ID of mate breakends"> | |
| 9 ##INFO=<ID=ISIZE,Number=.,Type=String,Description="Size of the SV"> | |
| 10 ##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record"> | |
| 11 ##FORMAT=<ID=lSC,Number=1,Type=Integer,Description="Length of the longest soft clips supporting the BND"> | |
| 12 ##FORMAT=<ID=nSC,Number=1,Type=Integer,Description="Number of supporting soft-clips"> | |
| 13 ##FORMAT=<ID=uRP,Number=1,Type=Integer,Description="Number of unmated read pairs nearby Soft-Clips"> | |
| 14 ##FORMAT=<ID=levD_local,Number=1,Type=Float,Description="Levenstein distance between soft-clipped bases and the area around the original soft-clipped site"> | |
| 15 ##FORMAT=<ID=levD_distl,Number=1,Type=Float,Description="Levenstein distance between the soft-clipped bases and mate location"> | |
| 16 ##FORMAT=<ID=CTX,Number=1,Type=Integer,Description="Number of chromosomal translocations"> | |
| 17 ##FORMAT=<ID=DEL,Number=1,Type=Integer,Description="Number of reads supporting Large Deletions"> | |
| 18 ##FORMAT=<ID=INS,Number=1,Type=Integer,Description="Number of reads supporting Large insertions"> | |
| 19 ##FORMAT=<ID=NOV_INS,Number=1,Type=Integer,Description="Number of reads supporting novel sequence insertion"> | |
| 20 ##FORMAT=<ID=TDUP,Number=1,Type=Integer,Description="Number of reads supporting a tandem duplication"> | |
| 21 ##FORMAT=<ID=INV,Number=1,Type=Integer,Description="Number of reads supporting inversions"> | |
| 22 ##FORMAT=<ID=sDEL,Number=1,Type=Integer,Description="Number of reads supporting novel sequence insertion"> | |
| 23 ##INFO=<ID=NO_MATE_SC,Number=1,Type=Flag,Description="When there is no softclipping of the mate read location, an appromiate position is used"> | |
| 24 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Dummy value for maintaining VCF-Spec"> | |
| 25 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT |