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VcfRebase
Pierre Lindenbaum edited this page Feb 23, 2015
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6 revisions
##Motivation
Finds restriction sites overlapping variants in a VCF file
see also Compilation.
$ make vcfrebase##Options
| Option | Description |
|---|---|
| -h | get help (this screen) |
| -v | print version and exit. |
| -L (level) | log level. One of java.util.logging.Level . |
| -R (file) | fasta sequence file indexed with picard. Required |
| -E (name) | restrict to that enzyme. Can be called multiple times. Optional |
| -w (float) | min enzyme weight (e.g: A=1, N=0.0, S=0.5) default=5.0 . Optional |
##Example
$ curl -s "ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/VCF/00-All.vcf.gz" |\
gunzip -c |\
java -jar dist/vcfrebase.jar -R human_g1k_v37.fasta -w 8 |\
grep -E '(#|ENZ=)'
##fileformat=VCFv4.1
##INFO=<ID=ENZ,Number=.,Type=String,Description="Enzyme overlapping: Format: (Name,Site,Sequence,pos-1,strand)">
(...)
#CHROM POS ID REF ALT QUAL FILTER INFO
1 256138 rs372711491 T G . . ENZ=(SwaI|ATTT^AAAT|ATTTAAAT|256139|+),(SwaI|ATTT^AAAT|ATTTAAAt|256131|+);OTHERKG;RS=372711491;RSPOS=256138;SAO=0;SSR=0;VC=SNV;VP=0x050000000001000002000100;WGT=1;dbSNPBuildID=138
1 744076 rs142181107 A C . . CAF=[0.9775,0.0225];COMMON=1;ENZ=(SwaI|ATTT^AAAT|ATTTAAaT|744070|+);KGPROD;KGPhase1;RS=142181107;RSPOS=744076;SAO=0;SSR=0;VC=SNV;VP=0x050000000001100014000100;WGT=1;dbSNPBuildID=134
1 762592 rs71507462 C G . . CAF=[0.2755,0.7245];COMMON=1;ENZ=(MauBI|CG^CGCGCG|cGCGCGCG|762592|+);GNO;KGPROD;KGPhase1;OTHERKG;R5;RS=71507462;RSPOS=762592;SAO=0;SLO;SSR=0;VC=SNV;VP=0x050100020001100116000100;WGT=1;dbSNPBuildID=130
1 780347 rs202219272 TTTAA T . . CAF=[0.9867,0.01331];COMMON=1;ENZ=(PacI|TTAAT^TAA|ttaaTTAA|780348|+);INT;KGPROD;KGPhase1;KGPilot123;OTHERKG;RS=202219272;RSPOS=780348;SAO=0;SSR=0;VC=DIV;VP=0x05000008000110001e000200;WGT=1;dbSNPBuildID=137
1 780361 rs111333032 A T . . ENZ=(SwaI|ATTT^AAAT|ATTTAAaT|780355|+);GNO;INT;OTHERKG;RS=111333032;RSPOS=780361;SAO=0;SLO;SSR=0;VC=SNV;VP=0x050100080001000102000100;WGT=1;dbSNPBuildID=132
1 786891 rs183914415 C T . . CAF=[0.9752,0.02479];COMMON=1;ENZ=(AscI|GG^CGCGCC|GGCGCGCC|786892|+);INT;KGPROD;KGPhase1;RS=183914415;RSPOS=786891;SAO=0;SSR=0;VC=SNV;VP=0x050000080001100014000100;WGT=1;dbSNPBuildID=135
1 820332 rs201213736 A G,T . . ENZ=(SwaI|ATTT^AAAT|ATTTAAaT|820326|+);OTHERKG;RS=201213736;RSPOS=820332;SAO=0;SSR=0;VC=SNV;VP=0x050000000001000002000100;WGT=1;dbSNPBuildID=137
1 820333 rs201439577 T C . . ENZ=(SwaI|ATTT^AAAT|ATTTAAAt|820326|+);OTHERKG;RS=201439577;RSPOS=820333;SAO=0;SSR=0;VC=SNV;VP=0x050000000001000002000100;WGT=1;dbSNPBuildID=137
1 822560 rs200342299 C T . . ENZ=(SfiI|GGCCNNNN^NGGCC|GGCCAGcTTGGCC|822554|+);OTHERKG;RS=200342299;RSPOS=822560;SAO=0;SSR=0;VC=SNV;VP=0x050000000001000002000100;WGT=1;dbSNPBuildID=137
1 822565 rs111427246 C T . . ENZ=(SfiI|GGCCNNNN^NGGCC|GGCCAGCTTGGcC|822554|+);GNO;OTHERKG;RS=111427246;RSPOS=822565;SAO=0;SLO;SSR=0;VC=SNV;VP=0x050100000001000102000100;WGT=1;dbSNPBuildID=132
1 837753 rs187865648 G A . . CAF=[0.9995,0.0004591];COMMON=0;ENZ=(SfiI|GGCCNNNN^NGGCC|gGCCATTCTGGCC|837753|+);KGPROD;KGPhase1;RS=187865648;RSPOS=837753;SAO=0;SSR=0;VC=SNV;VP=0x050000000001000014000100;WGT=1;dbSNPBuildID=135
1 839873 rs192553893 C T . . CAF=[0.6768,0.3232];COMMON=1;ENZ=(NotI|GC^GGCCGC|GcGGCCGC|839872|+);KGPROD;KGPhase1;OTHERKG;RS=192553893;RSPOS=839873;SAO=0;SSR=0;VC=SNV;VP=0x050000000001100016000100;WGT=1;dbSNPBuildID=135
1 839911 rs76652930 C T . . ASP;ENZ=(NotI|GC^GGCCGC|GcGGCCGC|839910|+);GNO;OTHERKG;RS=76652930;RSPOS=839911;SAO=0;SSR=0;VC=SNV;VP=0x050000000005000102000100;WGT=1;dbSNPBuildID=131
1 839912 rs369394889 GGCC G . . ENZ=(NotI|GC^GGCCGC|GCggccGC|839910|+);OTHERKG;RS=369394889;RSPOS=839913;SAO=0;SSR=0;VC=DIV;VP=0x050000000001000002000200;WGT=1;dbSNPBuildID=138
1 839933 rs146045242 C T . . CAF=[0.8852,0.1148];COMMON=1;ENZ=(NotI|GC^GGCCGC|GcGGCCGC|839932|+);KGPROD;KGPhase1;OTHERKG;RS=146045242;RSPOS=839933;SAO=0;SSR=0;VC=SNV;VP=0x050000000001100016000100;WGT=1;dbSNPBuildID=134
1 840009 rs140080750 C T . . CAF=[0.9692,0.03076];COMMON=1;ENZ=(NotI|GC^GGCCGC|GcGGCCGC|840008|+);KGPROD;KGPhase1;OTHERKG;RS=140080750;RSPOS=840009;SAO=0;SSR=0;VC=SNV;VP=0x050000000001100016000100;WGT=1;dbSNPBuildID=134