jvarkit

VCFBed

Transfer information from a BED to a VCF

Usage

This program is now part of the main jvarkit tool. See jvarkit for compiling.

Usage: java -jar dist/jvarkit.jar vcfbed  [options] Files

Usage: vcfbed [options] Files
  Options:
    --bcf-output
      If this program writes a VCF to a file, The format is first guessed from 
      the file suffix. Otherwise, force BCF output. The current supported BCF 
      version is : 2.1 which is not compatible with bcftools/htslib (last 
      checked 2019-11-15)
      Default: false
  * -B, --bed, -m, --map
      Tribble or Tabix bed file. Files must be indexed unless option --fast is 
      selected. 
    --bnd
      for SVTYPE=BND do not try to extend the interval to the variant and the 
      mate breakend.
      Default: false
    -e, --expr, --jexl, --format
      [20180124]A JEXL Expression returning a string JEXL stands for Java 
      EXpression Language.  See 
      https://commons.apache.org/proper/commons-jexl/reference/syntax.html . 
      The variable 'bed' is the current observed BedLine (see  https://github.com/lindenb/jvarkit/blob/7bddffca3899196e568fb5e1a479300c0038f74f/src/main/java/com/github/lindenb/jvarkit/util/bio/bed/BedLine.java 
      ).  The variable 'ctx' or 'variant' is the current observed variant. The 
      variable 'line' is the original bed line
      Default: bed.get(0)+":"+bed.get(1)+"-"+bed.get(2)
    --generate-vcf-md5
      Generate MD5 checksum for VCF output.
      Default: false
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -ignoreFiltered, --ignoreFiltered
      Ignore FILTERed Variants (should be faster)
      Default: false
    --limit
      limit number of annotations to that number. -1: unlimited
      Default: -1
    --fast, --memory
      Load files in memory (faster than tribble/tabix but memory consumming)
      Default: false
    -mofb, --min-overlap-bed-fraction
      Minimum overlap required as a fraction of BED record. A decimal number 
      between 0.0 and 1.0. If the value ends with '%' it is interpretted as a 
      percentage eg. '1%' => '0.01'. A slash '/' is interpretted as a ratio. 
      e.g: '1/100' => '0.01'.
    -mofr, --min-overlap-fraction
      Require that the minimum fraction be satisfied for VCF OR BED.A decimal 
      number between 0.0 and 1.0. If the value ends with '%' it is 
      interpretted as a percentage eg. '1%' => '0.01'. A slash '/' is 
      interpretted as a ratio. e.g: '1/100' => '0.01'.
    -mofv, --min-overlap-vcf-fraction
      Minimum overlap required as a fraction of VCF record. A decimal number 
      between 0.0 and 1.0. If the value ends with '%' it is interpretted as a 
      percentage eg. '1%' => '0.01'. A slash '/' is interpretted as a ratio. 
      e.g: '1/100' => '0.01'.
    -M, --mutual-fraction
      Mutual comparator Two SV have are the same if they share a fraction 'x' 
      of their bases. For very small SV the fraction can be quite small while 
      for large SV the fraction should be close to 1. The Syntax is the 
      following : (<MAX_SIZE_INCLUSIVE>:<FRACTION as double or percent>;)+ . 
      For example if the SV as a size of 99bp, the fraction used with be 0.6 
      for '10:0.1;100:0.6;1000:0.9'. For the smallest size, a simple overlap 
      is a positive match.. Example:"10:0.5;100:75%;1000:80%;10000:90%".
    -o, --out
      Output file. Optional . Default: stdout
    -T, --tag
      Name for the INFO tag name
      Default: VCFBED
    --version
      print version and exit
    -extend, --extend, --within-distance
      Variant and BED must be within 'x' bp.A distance specified as a positive 
      integer.Commas are removed. The following suffixes are interpreted : 
      b,bp,k,kb,m,mb,g,gb 
      Default: 0

Keywords

• bed
• vcf
• annotation

See also in Biostars

• https://www.biostars.org/p/247224

Creation Date

20180406

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/vcfbed/VCFBed.java

Unit Tests

https://github.com/lindenb/jvarkit/tree/master/src/test/java/com/github/lindenb/jvarkit/tools/vcfbed/VCFBedTest.java

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 vcfbed ? 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

Example

Map the NCBI biosystems to a BED file using the following script: https://gist.github.com/6024788

$ gunzip -c ~/ncbibiosystem.bed.gz | head
1	69091	70008	79501	106356	30	Signaling_by_GPCR
1	69091	70008	79501	106383	50	Olfactory_Signaling_Pathway
1	69091	70008	79501	119548	40	GPCR_downstream_signaling
1	69091	70008	79501	477114	30	Signal_Transduction
1	69091	70008	79501	498	40	Olfactory_transduction
1	69091	70008	79501	83087	60	Olfactory_transduction
1	367640	368634	26683	106356	30	Signaling_by_GPCR
1	367640	368634	26683	106383	50	Olfactory_Signaling_Pathway
1	367640	368634	26683	119548	40	GPCR_downstream_signaling
1	367640	368634	26683	477114	30	Signal_Transduction

Now, annotate a remote VCF with the data of NCBI biosystems.

curl "https://raw.github.com/arq5x/gemini/master/test/test1.snpeff.vcf" |\
 sed 's/^chr//' |\
 java -jar jvarkit.jar vcfbed -B ~/ncbibiosystem.bed.gz -T NCBIBIOSYS  -f '($4|$5|$6|$7)' |\
 grep -E '(^#CHR|NCBI)'

##INFO=<ID=NCBIBIOSYS,Number=.,Type=String,Description="metadata added from /home/lindenb/ncbibiosystem.bed.gz . Format was ($4|$5|$6|$7)">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	1094PC0005	1094PC0009	1094PC0012	1094PC0013
1	69270	.	A	G	2694.18	.	AC=40;AF=1.000;AN=40;DP=83;Dels=0.00;EFF=SYNONYMOUS_CODING(LOW|SILENT|tcA/tcG|S60|305|OR4F5|protein_coding|CODING|ENST00000335137|exon_1_69091_70008);FS=0.000;HRun=0;HaplotypeScore=0.0000;InbreedingCoeff=-0.0598;MQ=31.06;MQ0=0;NCBIBIOSYS=(79501|119548|40|GPCR_downstream_signaling),(79501|106356|30|Signaling_by_GPCR),(79501|498|40|Olfactory_transduction),(79501|83087|60|Olfactory_transduction),(79501|477114|30|Signal_Transduction),(79501|106383|50|Olfactory_Signaling_Pathway);QD=32.86	GT:AD:DP:GQ:PL	./.	./.	1/1:0,3:3:9.03:106,9,0	1/1:0,6:6:18.05:203,18,0
1	69511	.	A	G	77777.27	.	AC=49;AF=0.875;AN=56;BaseQRankSum=0.150;DP=2816;DS;Dels=0.00;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aca/Gca|T141A|305|OR4F5|protein_coding|CODING|ENST00000335137|exon_1_69091_70008);FS=21.286;HRun=0;HaplotypeScore=3.8956;InbreedingCoeff=0.0604;MQ=32.32;MQ0=0;MQRankSum=1.653;NCBIBIOSYS=(79501|119548|40|GPCR_downstream_signaling),(79501|106356|30|Signaling_by_GPCR),(79501|498|40|Olfactory_transduction),(79501|83087|60|Olfactory_transduction),(79501|477114|30|Signal_Transduction),(79501|106383|50|Olfactory_Signaling_Pathway);QD=27.68;ReadPosRankSum=2.261	GT:AD:DP:GQ:PL	./.	./.	0/1:2,4:6:15.70:16,0,40	0/1:2,2:4:21.59:22,0,40</h:pre>

Another example:

$ tabix -h dbsnp138_00-All.vcf.gz "19:58864565-58865165" | sed '/^[^#]/s/^/chr/' |\
java -jar dist/vcfbed.jar -m your.bed -e 'bed.get(0)+"|"+bed.get(1)+"|"+bed.get(2)+"|"+bed.get(3)+"&"+bed.get(4)'

##INFO=<ID=VCFBED,Number=.,Type=String,Description="metadata added from your.bed . Format was ${1}|${2}|${3}|${4}&${5}">
(...)
chr19   58864911    rs113760967 T   C   .   .   GNO;OTHERKG;R5;RS=113760967;RSPOS=58864911;SAO=0;SLO;SSR=0;VC=SNV;VCFBED=chr19|58864565|58865165|A1BG&58864865;VP=0x050100020001000102000100;WGT=1;dbSNPBuildID=132
chr19   58865054    rs893183    T   C   .   .   CAF=[0.1299,0.8701];COMMON=1;G5;GNO;HD;KGPROD;KGPhase1;KGPilot123;OTHERKG;PH3;R5;RS=893183;RSPOS=58865054;RV;SAO=0;SLO;SSR=0;VC=SNV;VCFBED=chr19|58864565|58865165|A1BG&58864865;VLD;VP=0x05010002000115051f000100;WGT=1;dbSNPBuildID=86
chr19   58865068    rs893182    T   C   .   .   CAF=[0.1299,0.8701];COMMON=1;G5;GNO;HD;KGPROD;KGPhase1;KGPilot123;OTHERKG;PH3;R5;RS=893182;RSPOS=58865068;RV;SAO=0;SLO;SSR=0;VC=SNV;VCFBED=chr19|58864565|58865165|A1BG&58864865;VLD;VP=0x05010002000115051f000100;WGT=1;dbSNPBuildID=86
chr19   58865082    rs893181    A   T   .   .   CAF=[0.1295,0.8705];COMMON=1;G5;GNO;HD;KGPROD;KGPhase1;KGPilot123;OTHERKG;PH3;R5;RS=893181;RSPOS=58865082;RV;SAO=0;SLO;SSR=0;VC=SNV;VCFBED=chr19|58864565|58865165|A1BG&58864865;VLD;VP=0x05010002000115051f000100;WGT=1;dbSNPBuildID=86
chr19   58865091    rs893180    A   G   .   .   CAF=[0.1299,0.8701];COMMON=1;G5;GNO;HD;KGPROD;KGPhase1;KGPilot123;OTHERKG;R5;RS=893180;RSPOS=58865091;RV;SAO=0;SLO;SSR=0;VC=SNV;VCFBED=chr19|58864565|58865165|A1BG&58864865;VLD;VP=0x05010002000115051e000100;WGT=1;dbSNPBuildID=86
chr19   58865112    rs188818621 C   T   .   .   CAF=[0.9954,0.004591];COMMON=1;KGPROD;KGPhase1;R5;RS=188818621;RSPOS=58865112;SAO=0;SSR=0;VC=SNV;VCFBED=chr19|58864565|58865165|A1BG&58864865;VP=0x050000020001000014000100;WGT=1;dbSNPBuildID=135
chr19   58865164    rs80109863  C   T   .   .   CAF=[0.9949,0.005051];COMMON=1;GNO;KGPROD;KGPhase1;OTHERKG;R5;RS=80109863;RSPOS=58865164;SAO=0;SSR=0;VC=SNV;VCFBED=chr19|58864565|58865165|A1BG&58864865;VP=0x050000020001000116000100;WGT=1;dbSNPBuildID=132

Cited in

• Megquier K, Turner-Maier J, Morrill K, Li X, Johnson J, Karlsson EK, et al. (2022) The genomic landscape of canine osteosarcoma cell lines reveals conserved structural complexity and pathway alterations. PLoS ONE 17(9): e0274383. https://doi.org/10.1371/journal.pone.0274383

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