jvarkit
VcfToBed
vcf to bed
Usage
Usage: vcf2bed [options] Files
Options:
-F, --format
output format
Default: bed
Possible Values: [bed, interval]
-header, --header
Print Header
Default: false
-h, --help
print help and exit
--helpFormat
What kind of help. One of [usage,markdown,xml].
-M, --max
Optional filter: max sequence length. A distance specified as a positive
integer.Commas are removed. The following suffixes are interpreted :
b,bp,k,kb,m,mb
-m, --min
Optional filter: min sequence length. A distance specified as a positive
integer.Commas are removed. The following suffixes are interpreted :
b,bp,k,kb,m,mb
-c, --no-ci
For structural variant, ignore the extention of the boundaries using
INFO/CIPOS and INFO/CIEND
Default: false
-o, --output
Output file. Optional . Default: stdout
-R, --reference, --dict
A SAM Sequence dictionary source: it can be a *.dict file, a fasta file
indexed with 'picard CreateSequenceDictionary', or any hts file
containing a dictionary (VCF, BAM, CRAM, intervals...)
-x, --slop
Extends interval. Extending interval. The following syntaxes are
supported: 1000; 1kb; 1,000; 30%(shrink); 150% (extend); 0.5 (shrink);
1.5 (extend)
Default: 0
--version
print version and exit
Keywords
- bed
- vcf
Compilation
Requirements / Dependencies
- java compiler SDK 11. Please check that this java is in the
${PATH}. Setting JAVA_HOME is not enough : (e.g: https://github.com/lindenb/jvarkit/issues/23 )
Download and Compile
$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ ./gradlew vcf2bed
The java jar file will be installed in the dist directory.
Creation Date
20181203
Source code
Unit Tests
Contribute
- Issue Tracker: http://github.com/lindenb/jvarkit/issues
- Source Code: http://github.com/lindenb/jvarkit
License
The project is licensed under the MIT license.
Citing
Should you cite vcf2bed ? https://github.com/mr-c/shouldacite/blob/master/should-I-cite-this-software.md
The current reference is:
http://dx.doi.org/10.6084/m9.figshare.1425030
Lindenbaum, Pierre (2015): JVarkit: java-based utilities for Bioinformatics. figshare. http://dx.doi.org/10.6084/m9.figshare.1425030
Motivation
I’m lazy about using awk or bioalcidaejdk for this task and I want something that uses INFO/CIPOS and INFO/CIEND for structural variants
Input
input is one or more VCF file
one file ending with ‘.list’ is interpreted as a list of paths (one per lines)
one file ending with ‘.zip’ or ‘.tar’ or ‘.tar.gz’ is interpreted an archive and all the files looking like vcf files are extracted
if there is no input, the program reads vcf from stdin
##Example
$ wget -q -O - "https://github.com/hall-lab/cshl_sv_2014/blob/master/supplemental/NA12878.lumpy.vcf?raw=true" |\
grep -A 10 '#CHROM'
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878
1 869423 1 G <DEL> 345.50 . SVTYPE=DEL;SVLEN=-857;END=870280;STR=+-:25;IMPRECISE;CIPOS=-1,34;CIEND=0,0;EVENT=1;SUP=25;PESUP=25;SRSUP=0;EVTYPE=PE;PRIN GT:SUP:PE:SR:GQ:DP:RO:AO:SQ:GL 1/1:25:25:0:0.00:71:19:52:345.50:-36,-8,-1
1 1588585 5 A <DUP> 0.00 . SVTYPE=DUP;SVLEN=65356;END=1653941;STR=-+:7;IMPRECISE;CIPOS=-126,1;CIEND=-2,67;EVENT=5;SUP=7;PESUP=7;SRSUP=0;EVTYPE=PE;PRIN GT:SUP:PE:SR:GQ:DP:RO:AO:SQ:GL 0/1:7:7:0:74.40:139:125:13:0.00:-1,-8,-24
1 1594964 6 C <DUP> 0.00 . SVTYPE=DUP;SVLEN=65855;END=1660819;STR=-+:8;IMPRECISE;CIPOS=-81,2;CIEND=-1,127;EVENT=6;SUP=8;PESUP=8;SRSUP=0;EVTYPE=PE;PRIN GT:SUP:PE:SR:GQ:DP:RO:AO:SQ:GL 0/1:8:8:0:77.96:153:137:15:0.00:-1,-9,-25
1 2566176 7 A <DEL> 121.20 . SVTYPE=DEL;SVLEN=-418;END=2566594;STR=+-:14;IMPRECISE;CIPOS=-2,68;CIEND=0,0;EVENT=7;SUP=14;PESUP=14;SRSUP=0;EVTYPE=PE;PRIN GT:SUP:PE:SR:GQ:DP:RO:AO:SQ:GL 0/1:14:14:0:0.00:78:44:33:121.20:-13,-1,-12
1 2911548 8 G <DEL> 440.34 . SVTYPE=DEL;SVLEN=-302;END=2911850;STR=+-:20;CIPOS=0,0;CIEND=0,0;EVENT=8;SUP=20;PESUP=8;SRSUP=12;EVTYPE=PE,SR;PRIN GT:SUP:PE:SR:GQ:DP:RO:AO:SQ:GL 0/1:20:8:12:0.00:185:86:99:440.34:-48,-4,-15
1 2919034 9 G <DEL> 289.83 . SVTYPE=DEL;SVLEN=-332;END=2919366;STR=+-:22;CIPOS=0,0;CIEND=0,0;EVENT=9;SUP=22;PESUP=10;SRSUP=12;EVTYPE=PE,SR;PRIN GT:SUP:PE:SR:GQ:DP:RO:AO:SQ:GL 0/1:22:10:12:0.00:160:86:74:289.83:-31,-2,-20
1 5447229 14 G <DUP> 380.12 . SVTYPE=DUP;SVLEN=210;END=5447439;STR=-+:11;CIPOS=0,0;CIEND=0,0;EVENT=14;SUP=11;PESUP=1;SRSUP=10;EVTYPE=PE,SR;PRIN GT:SUP:PE:SR:GQ:DP:RO:AO:SQ:GL 1/1:11:1:10:0.00:197:104:93:380.12:-39,-7,-1
1 5876603 15 G <DEL> 0.00 . SVTYPE=DEL;SVLEN=-928;END=5877531;STR=+-:8;CIPOS=0,0;CIEND=0,0;EVENT=15;SUP=8;PESUP=0;SRSUP=8;EVTYPE=SR;PRIN GT:SUP:PE:SR:GQ:DP:RO:AO:SQ:GL 0/1:8:0:8:294.07:169:168:0:0.00:-8,-37,-117
1 5877530 16 T <DEL> 63.31 . SVTYPE=DEL;SVLEN=-72;END=5877602;STR=+-:13;CIPOS=0,0;CIEND=0,0;EVENT=16;SUP=13;PESUP=0;SRSUP=13;EVTYPE=SR;PRIN GT:SUP:PE:SR:GQ:DP:RO:AO:SQ:GL 0/1:13:0:13:0.00:188:136:51:63.31:-10,-4,-54
1 6619067 19_1 T [1:6619506[T 0.00 . SVTYPE=BND;STR=--:7;IMPRECISE;CIPOS=-88,1;CIEND=-26,2;MATEID=19_2;EVENT=19;SUP=7;PESUP=7;SRSUP=0;EVTYPE=PE;PRIN GT:SUP:PE:SR:GQ:DP:RO:AO:SQ:GL 0/1:7:7:0:127.76:131:117:13:0.00:-1,-14,-66
$ wget -q -O - "https://github.com/hall-lab/cshl_sv_2014/blob/master/supplemental/NA12878.lumpy.vcf?raw=true" |\
java -jar dist/vcf2bed.jar |\
head
1 869421 870280 1 345
1 1588458 1654008 5 0
1 1594882 1660946 6 0
1 2566173 2566594 7 121
1 2911547 2911850 8 440
1 2919033 2919366 9 289
1 5447228 5447439 14 380
1 5876602 5877531 15 0
1 5877529 5877602 16 63
1 6618978 6619069 19_1 0
With tar.gz
$ tar cvfz ~/jeter.tar.gz src/test/resources/rotavirus_rf.*.vcf.gz
$ tar tvfz ~/jeter.tar.gz
-rw-r--r-- lindenb/lindenb 5805 2019-01-11 18:29 src/test/resources/rotavirus_rf.ann.vcf.gz
-rw-r--r-- lindenb/lindenb 27450 2019-01-11 18:29 src/test/resources/rotavirus_rf.freebayes.vcf.gz
-rw-r--r-- lindenb/lindenb 7366 2019-01-11 18:29 src/test/resources/rotavirus_rf.unifiedgenotyper.vcf.gz
With zip
$ zip ~/jeter.zip src/test/resources/rotavirus_rf.*.vcf.gz
$ tar tvfz ~/jeter.tar.gz
-rw-r--r-- lindenb/lindenb 5805 2019-01-11 18:29 src/test/resources/rotavirus_rf.ann.vcf.gz
-rw-r--r-- lindenb/lindenb 27450 2019-01-11 18:29 src/test/resources/rotavirus_rf.freebayes.vcf.gz
-rw-r--r-- lindenb/lindenb 7366 2019-01-11 18:29 src/test/resources/rotavirus_rf.unifiedgenotyper.vcf.gz
$ java -jar dist/vcf2bed.jar ~/jeter.zip | wc