My tool to annotate VCF files.

The Variant Call Format is a text file format generated by many tools for NGS. It contains meta-information lines, a header line, and then data lines describing how the mutations were called. I don't like this format because it cannot be used to store some hierachical annotations (like json or xml), nevertheless it is a de facto standard.

I wrote a tool called vcfannotator to append a set of annotations from the UCSC database to a VCF file. As I wanted to keep this tool simple and without any dependencies, it only uses the flat files available from the download area at the UCSC.

This tools appends several informations:

• A prediction of the mutation: is it in the cDNA ? in an intron ? in an exon ? is it a non-synonymous mutation ? was a stop codon lost or gained ? is there any consequence on the splicing process ? Here, the UCSC DAS server and the KnonwGenes table are used to retrieve the genomic DNA and the structure of the gene.
• dbSNP: was this mutation found before in dbSNP ?
• Personal genomes: was this mutation found before in Venter's genome ? In Watson's genome ? etc...
• The mapability (Uniqueness of Reference Genome ): gives an idea about how the context is unique in the genome
• genomicSuperDups: is this mutation located in a segmental genomic duplication ?
• tfbsConsSites: is this mutation located in the site of a transcription factor ?
• phastCons44way: how is the mutation conserved within a multiple alignments of 44 vertebrate genomes to the human genome ?

The tool is available on github at: https://github.com/lindenb/jsandbox in jsandbox/src/sandbox/VCFAnnotator.java.

Compilation

> cd jsandbox
> ant vcfannotator

Execution & Options

> java -jar dist/vcfannotator.jar -h
VCF annotator
Pierre Lindenbaum PhD. 2010. http://plindenbaum.blogspot.com
Options:
-b ucsc.build default:hg18
-m mapability.
-g genomicSuperDups
-p basic prediction
-c phastcons prediction (phastCons44way)
-t transcription factors sites prediction
-pg personal genomes
-snp <id> add ucsc <id> must be present in "http://hgdownload.cse.ucsc.edu/goldenPath/<ucscdb>/database/<id>.txt.gz" e.g. snp129
-log <level> one value from java.util.logging.Level default:OFF
-proxyHost <host>
-proxyPort <port>

Example

Input

##fileformat=VCFv3.2
##fileDate=20091120
##source=gigabayes
##reference=ncbi36
##phasing=none
#CHROM POS ID REF ALT QUAL FILTER INFO
1 1105366 . T C 99 0 NS=471;DP=16179;AC=8;AN=942;HWE=0.0685233
1 1105373 . C T 99 0 NS=469;DP=15318;AC=5;AN=938;HWE=0.0267954
1 1108138 rs61733845 C T 99 0 NS=450;DP=16134;AC=110;AN=900;dbSNP;HWE=0.930276
1 1109206 . G A 99 0 NS=696;DP=54701;AC=2;AN=1392;HWE=0.0028777
1 1109262 . C T 99 0 NS=696;DP=55783;AC=12;AN=1392;HWE=0.104349
1 1110233 . C G 99 0 NS=694;DP=34301;AC=43;AN=1388;HWE=4.91397
1 1110240 . T A 99 0 NS=695;DP=35846;AC=3;AN=1390;HWE=0.00648883
1 1110294 rs1320571 G A 99 0 NS=608;DP=36050;AC=246;AN=1216;dbSNP;HM;HWE=3.05358
1 1110351 . A C 99 0 NS=696;DP=26284;AC=15;AN=1392;HWE=0.163402
1 1110358 . T C 99 0 NS=694;DP=24596;AC=24;AN=1388;HWE=0.422309
1 1110366 . G A 99 0 NS=697;DP=22511;AC=16;AN=1394;HWE=0.185781
1 3537495 . C T 99 0 NS=697;DP=25302;AC=15;AN=1394;HWE=0.163165
1 3537910 . G A 99 0 NS=605;DP=15896;AC=34;AN=1210;HWE=0.46683
1 3537996 rs2760321 T C 99 0 NS=571;DP=15376;AC=1040;AN=1142;dbSNP;HM;HWE=4.28852
(...)

Command:

java -jar dist/vcfannotator.jar -pg -m -g -p -c -t -snp snp130 -log ALL input.vcf
## wait !

Result

##fileformat=VCFv3.2
##fileDate=20091120
##source=gigabayes
##reference=ncbi36
##phasing=none
##SNP130=table snp130 from UCSC
##INFO=NA12878,1,String,"NA12878's Personal genome"
##INFO=NA12891,1,String,"NA12891's Personal genome"
(...)
chr1 1108138 rs61733845 C T 99 0 NS=450;DP=16134;AC=110;AN=900;dbSNP;HWE=0.930276;MAPABILITY_WGENCODEBROADMAPABILITYALIGN36MER=1;MAPABILITY_WGENCODEDUKEUNIQUENESS20=1;MAPABILITY_WGENCODEDUKEUNIQUENESS24=1;MAPABILITY_WGENCODEDUKEUNIQUENESS35=1;phastCons44way=1.000;PREDICTION=geneSymbol:TTLL10|wild.codon:TGC|wild.aa:C|pos.cdna:935|kgId:uc001acy.1|position.protein:312|strand:+|mut.aa:C|mut.codon:TGT|exon.name:Exon 11|type:EXON_CODING_SYNONYMOUS;PREDICTION=geneSymbol:TTLL10|wild.codon:TGC|wild.aa:C|pos.cdna:716|kgId:uc001acz.1|position.protein:239|strand:+|mut.aa:C|mut.codon:TGT|exon.name:Exon 7|type:EXON_CODING_SYNONYMOUS
(...)
chr1 1110351 . A C 99 0 NS=696;DP=26284;AC=15;AN=1392;HWE=0.163402;MAPABILITY_WGENCODEBROADMAPABILITYALIGN36MER=1;MAPABILITY_WGENCODEDUKEUNIQUENESS20=1;MAPABILITY_WGENCODEDUKEUNIQUENESS24=1;MAPABILITY_WGENCODEDUKEUNIQUENESS35=1;phastCons44way=1.000;PREDICTION=geneSymbol:TTLL10|wild.codon:AAG|wild.aa:K|splicing:SPLICING_DONOR|pos.cdna:1399|kgId:uc001acy.1|position.protein:467|strand:+|mut.aa:T|mut.codon:ACG|exon.name:Exon 13|type:EXON_CODING_NON_SYNONYMOUS;PREDICTION=geneSymbol:TTLL10|wild.codon:AAG|wild.aa:K|pos.cdna:1180|kgId:uc001acz.1|position.protein:394|strand:+|mut.aa:T|mut.codon:ACG|exon.name:Exon 9|type:EXON_CODING_NON_SYNONYMOUS
(...)
chr1 113068276 . C G 99 0 NS=697;DP=12774;AC=7;AN=1394;HWE=0.0353282;MAPABILITY_WGENCODEBROADMAPABILITYALIGN36MER=1;MAPABILITY_WGENCODEDUKEUNIQUENESS20=1;MAPABILITY_WGENCODEDUKEUNIQUENESS24=1;MAPABILITY_WGENCODEDUKEUNIQUENESS35=1;phastCons44way=1.000;PREDICTION=geneSymbol:FAM19A3|wild.codon:CCA|wild.aa:P|pos.cdna:451|kgId:uc001ecu.1|position.protein:151|strand:+|mut.aa:R|mut.codon:CGA|exon.name:Exon 4|type:EXON_CODING_NON_SYNONYMOUS;PREDICTION=geneSymbol:FAM19A3|wild.codon:ACC|wild.aa:T|pos.cdna:383|kgId:uc001ecv.1|position.protein:128|strand:+|mut.aa:T|mut.codon:ACG|exon.name:Exon 4|type:EXON_CODING_SYNONYMOUS
(...)

Interestingly, for this last mutation chr1:113068276, there are two transcripts at the same position with two different translation frames, so there are two predictions: one synonymous mutation and one non-synonymous mutation.


That's it,

Pierre