VcfRebase

##Motivation

Finds restriction sites overlaping variants

##Compilation

Requirements / Dependencies

java 1.8 http://www.oracle.com/technetwork/java/index.html (NOT the old java 1.7 or 1.6) . Please check that this java is in the ${PATH}. Setting JAVA_HOME is not enough : (e.g: https://github.com/lindenb/jvarkit/issues/23 )
GNU Make > 3.81
curl/wget
git
apache ant is only required to compile htsjdk
xsltproc http://xmlsoft.org/XSLT/xsltproc2.html

Download and Compile

$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ make vcfrebase

by default, the libraries are not included in the jar file, so you shouldn't move them (https://github.com/lindenb/jvarkit/issues/15#issuecomment-140099011 ). You can create a bigger but standalone executable jar by addinging standalone=yes on the command line:

$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ make vcfrebase standalone=yes

The required libraries will be downloaded and installed in the dist directory.

edit 'local.mk' (optional)

The a file local.mk can be created edited to override/add some paths.

For example it can be used to set the HTTP proxy:

http.proxy.host=your.host.com
http.proxy.port=124567

##Synopsis

$ java -jar dist/vcfrebase.jar  [options] (stdin|file.vcf|file.vcf.gz)

Options

-o|--output (OUTPUT-FILE) Output file. Default:stdout
-R|--REF (FASTA) indexed Fasta sequence
-E|--enzyme (VALUE) restrict to that enzyme. Can be called multiple timesMultiple calls to this option should end with double hyphen : --
-w|--enzyme (VALUE) min enzyme weight (e.g: A=1, N=0.0, S=0.5) Default value : "5f".
-h|--help print help
-version|--version show version and exit

##Source Code

Main code is: https://github.com/lindenb/jvarkit/blob/master/src/main/java/com/github/lindenb/jvarkit/tools/vcfrebase/VcfRebase.java

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