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JVARKIT

Java utilities for Next Generation Sequencing

Pierre Lindenbaum PhD

http://plindenbaum.blogspot.com

@yokofakun

Dependencies

Tested with java 1.7 and the Picard library 1.91 ( http://sourceforge.net/projects/picard/)

Download & Install

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

edit build.properties to configure the project. Something like:

picard.version=1.91
picard.dir=/home/lindenb/package/picard-tools-${picard.version}
picard.jar=${picard.dir}/picard-${picard.version}.jar
sam.jar=${picard.dir}/sam-${picard.version}.jar
variant.jar=${picard.dir}/variant-${picard.version}.jar
tribble.jar=${picard.dir}/tribble-${picard.version}.jar

Working behind a proxy ? Edit the file build.dtd. Change it to:

<!ENTITY httpProxyHost "proxy-upgrade.univ-nantes.prive">
<!ENTITY httpProxyPort "3128">
<!ENTITY xjcproxyarg " <arg value='-httpproxy'/> <arg value='&httpProxyHost;:&httpProxyPort;'/>">
(...)

no proxy, set build.dtd to

<!ENTITY httpProxyHost "">
<!ENTITY httpProxyPort "">
<!ENTITY xjcproxyarg "">
(...)

Tools

Filtering VCF with javascript (rhino)

Compilation

``` ant vcffilterjs ```

Usage

``` java -jar dist/vcffilterjs.jar [options] ```

Options

OptionDescription
SCRIPT_FILE=Filejavascript file Default value: null.
SCRIPT_EXPRESSION=Stringjavascript expression Default value: null.
IN=StringVCF file/URL to process. Default stdin. Default value: null.
OUT=FileVCF file to generate. Default stdout. Default value: null.

the script binds the following variables:

the script should return '1' or true if the current VCF file should be printed.

Example

the file filter.js

/** prints a VARIATION if two samples at least
have a DP<200 */ 
function myfilterFunction()
	{
	var samples=header.genotypeSamples;
	var countOkDp=0;


	for(var i=0; i< samples.size();++i)
		{
		var sampleName=samples.get(i);
		if(! variant.hasGenotype(sampleName)) continue;
		var genotype = variant.genotypes.get(sampleName);
		if( ! genotype.hasDP()) continue;
		var dp= genotype.getDP();
		if(dp < 200 ) countOkDp++;
		}
	return (countOkDp>2)
	}
myfilterFunction();
$ curl -s "https://raw.github.com/jamescasbon/PyVCF/master/vcf/test/gatk.vcf" |\
   java -jar  dist/vcffilterjs.jar  SCRIPT_FILE=filter.js
   
##fileformat=VCFv4.1
##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	BLANK	NA12878	NA12891	NA12892	NA19238	NA19239	NA19240
chr22	42526449	.	T	A	151.47	.	AC=1;AF=0.071;AN=14;BaseQRankSum=2.662;DP=1226;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=41.2083;MQ=240.47;MQ0=0;MQRankSum=0.578;QD=4.89;ReadPosRankSum=3.611	GT:AD:DP:GQ:PL	0/1:23,8:31:99:190,0,694	0/0:188,0:190:99:0,478,5376	0/0:187,0:187:99:0,493,5322	0/0:247,0:249:99:0,634,6728	0/0:185,0:185:99:0,487,5515	0/0:202,0:202:99:0,520,5857	0/0:181,1:182:99:0,440,5362
chr22	42526634	.	T	C	32.60	.	AC=1;AF=0.071;AN=14;BaseQRankSum=1.147;DP=1225;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=50.0151;MQ=240.65;MQ0=0;MQRankSum=1.151;QD=1.30;ReadPosRankSum=1.276	GT:AD:DP:GQ:PL	0/1:21,4:25:71:71,0,702	0/0:187,2:189:99:0,481,6080	0/0:233,0:233:99:0,667,7351	0/0:230,0:230:99:0,667,7394	0/0:174,1:175:99:0,446,5469	0/0:194,2:196:99:0,498,6239	0/0:174,0:175:99:0,511,5894
chr22	42527793	rs1080989	C	T	3454.66	.	AC=2;AF=0.167;AN=12;BaseQRankSum=-3.007;DB;DP=1074;DS;Dels=0.01;FS=0.000;HRun=1;HaplotypeScore=75.7865;MQ=209.00;MQ0=0;MQRankSum=3.014;QD=9.36;ReadPosRankSum=0.618	GT:AD:DP:GQ:PL	./.	0/1:72,90:162:99:1699,0,1767	0/1:103,96:202:99:1756,0,2532	0/0:188,0:188:99:0,526,5889	0/0:160,0:160:99:0,457,4983	0/0:197,0:198:99:0,544,6100	0/0:156,0:156:99:0,439,5041

compile

$ ant vcffilterjs 
Buildfile: /home/lindenb/src/jvarkit-git/build.xml

vcffilterjs:
    (...)

BUILD SUCCESSFUL
Total time: 1 second

SAM4WebLogo

Motivation

"Sequence logo ( http://weblogo.berkeley.edu/logo.cgi ) for different alleles or generated from SAM/BAM" http://www.biostars.org/p/73021

ScreenShot

Compilation

ant sam4weblogo

Options

  • INPUT=File A BAM file to process. Required.
  • REGION=String Region to observe: chrom:start-end Required.

Example

```bash $ java -jar dist/sam4weblogo.jar I=path/to/samtools-0.1.18/examples/sorted.bam R=seq1:80-110 2> /dev/null | head -n 50 >B7_593:4:106:316:452/1 TGTTG-------------------------- >B7_593:4:106:316:452a/1 TGTTG-------------------------- >B7_593:4:106:316:452b/1 TGTTG-------------------------- >B7_589:8:113:968:19/2 TGGGG-------------------------- >B7_589:8:113:968:19a/2 TGGGG-------------------------- >B7_589:8:113:968:19b/2 TGGGG-------------------------- >EAS54_65:3:321:311:983/1 TGTGGG------------------------- >EAS54_65:3:321:311:983a/1 TGTGGG------------------------- >EAS54_65:3:321:311:983b/1 TGTGGG------------------------- >B7_591:6:155:12:674/2 TGTGGGGG----------------------- >B7_591:6:155:12:674a/2 TGTGGGGG----------------------- >B7_591:6:155:12:674b/2 TGTGGGGG----------------------- >EAS219_FC30151:7:51:1429:1043/2 TGTGGGGGGCGCCG----------------- >EAS219_FC30151:7:51:1429:1043a/2 TGTGGGGGGCGCCG----------------- >EAS219_FC30151:7:51:1429:1043b/2 TGTGGGGGGCGCCG----------------- >B7_591:5:42:540:501/1 TGTGGGGGCCGCAGTG--------------- >EAS192_3:5:223:142:410/1 TGGGGGGGGCGCAGT---------------- >B7_591:5:42:540:501a/1 TGTGGGGGCCGCAGTG--------------- >EAS192_3:5:223:142:410a/1 TGGGGGGGGCGCAGT---------------- >B7_591:5:42:540:501b/1 TGTGGGGGCCGCAGTG--------------- >EAS192_3:5:223:142:410b/1 TGGGGGGGGCGCAGT---------------- ```

SAM2Tsv

display a tabular view of each base of the reads vs the reference.

Compilation

```bash ant sam2tsv ```

Options

  • IN=File BAM files to process. This option may be specified 0 or more times.
  • REGION=String restrict to that region (chr:start-end) Default value: null.
  • REF=File Indexed reference Required.
  • A={true,false} Use Alignment format.

Example

```bash java -jar dist/sam2tsv.jar \ I=sorted.bam \ R=genome.fa \ L=chr1:32944435-32944435

M00491:12:000000000-A3FL3:1:1101:16929:4287 147 1 A 20 chr22 544289 A M = M00491:12:000000000-A3FL3:1:1101:16929:4287 147 2 G 28 chr22 544290 G M = M00491:12:000000000-A3FL3:1:1101:16929:4287 147 3 A 32 chr22 544291 C M X M00491:12:000000000-A3FL3:1:1101:16929:4287 147 4 T 37 chr22 544292 T M = M00491:12:000000000-A3FL3:1:1101:16929:4287 147 5 C 36 chr22 544293 C M =


<br/>
<h3>cmpbam: Comparing two or more BAMS</h3>

<h4>Compilation</h4>
```bash
ant cmpbams

Options

OptionDescription
IN=FileBAM files to process. This option must be specified at least 2 times.
REGION=Stringrestrict to that region (chr:start-end) Default value: null.
USESAMFLAG=Booleanuse SAM Flag when comparing. Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false}

Example

```bash java -jar dist/cmpbams.ja \ I=file1.bam \ I=file2.bam \ I=file3.bam \ L=chr1:32944435-32944435 ```

Bam2Raster

(under development)

Motivation

Save a BAM alignment as a PNG image.

Options

OptionDescription
IN=FileBAM files to process. Required.
OUT=FileImage name. Required.
REGION=Stringrestrict to that region (chr:start-end) Default value: null.
REF=FileIndexex reference Required.
WIDTH=Integerimage width Default value: 1000. This option can be set to 'null' to clear the default value.
NAME=Booleanprint read name. Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false}
BASE=Booleanprint base. Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false}

Compilation

```bash ant bam2raster ```

Example

```bash java -jar dist/bam2raster.jar \ IN=sorted.bam L=seq1:200-300 \ OUT=ouput.png \ R=ex1.fa ``` ![ScreenShot](https://raw.github.com/lindenb/jvarkit/master/doc/bam2graphics.png)

VCF2SQL

Motivation

Generate the SQL code to insert a VCF into sqlite3.

Options

OptionDescription
IN=FileVCF files to process. This option may be specified 0 or more times.
SUFFIX=StringTable suffix Default value: (empty).
USE_VEP=BooleanUse and explode VEP predictions Default value: true. Possible values: {true, false}
USE_SNPEFF=BooleanUse and explode SNPEFF predictions Default value: true. Possible values: {true, false}
ENGINE=Stringsql engine [sqlite,hsql] Default value: sqlite. This option can be set to 'null' to clear the default value.
SPLIT4=BooleanSplit DP4 Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false}

Example

```bash java -jar dist/vcf2sql.jar I=file.vcf | sqlite3 db.sqlite ```

Compilation

```bash ant vcf2sql ```

Schema

![Schema](https://chart.googleapis.com/chart?cht=gv&chl=digraph{HEADER->FILE;VARIATION->FILE;ALT->VARIATION;FILTER->VARIATION;INFO->VARIATION;SAMPLE->GENOTYPE;GENOTYPE->VARIATION;GTPROP->GENOTYPE;EXTRAINFO->INFO;EXTRAINFOPROP->EXTRAINFO;})

SortVCFOnRef

Motivation

Sort a VCF using the reference order. Version: 1.0

Options

OptionDescription
IN=FileVCF file (or stdin). Default value: null.
OUT=Fileoutput file (or stdout). Default value: null.
REF=FileReference file. Required.

Example

```bash java -jar dist/sortvcfonref.jar I=in.vcf O=out.vcf REF=ref.fa ```

Compilation

```bash ant sortvcfonref ```

SamJS: filtering a SAM/BAM file with javascript.

Motivation

Filters a BAM using javascript( java rhino engine).

Scripting

The script puts 'record' a SamRecord (http://picard.sourceforge.net/javadoc/net/sf/samtools/SAMRecord.html) and 'header' ( http://picard.sourceforge.net/javadoc/net/sf/samtools/SAMFileHeader.html) in the script context

Options

OptionDescription
IN=FileBAM file to process. Default stdin.
OUT=Fileoutput filename. Default stdin.
SCRIPT_FILE=Filejavascript file
SCRIPT_EXPRESSION=Stringjavascript expression
SAM_OUTPUT=Booleansam output Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false}
LIMIT=Longlimit to 'L' records.

Compilation

```bash ant samjs ```

Example

get a SAM where the read OR the mate is unmapped 
java -jar dist/samjs.jar I=ex1.bam \
	VALIDATION_STRINGENCY=SILENT \
	SCRIPT_EXPRESSION="record.readUnmappedFlag || record.mateUnmappedFlag;" \
	SAM=true 

@HD	VN:1.4	SO:unsorted
@SQ	SN:seq1	LN:1575
@SQ	SN:seq2	LN:1584
B7_591:4:96:693:509	73	seq1	1	99	36M	*	0	0	CACTAGTGGCTCATTGTAAATGTGTGGTTTAACTCG	<<<<<<<<<<<<<<<;<<<<<<<<<5<<<<<;:<;7	H0:i:1	H1:i:0	MF:i:18	NM:i:0	UQ:i:0	Aq:i:73
EAS54_65:7:152:368:113	73	seq1	3	99	35M	*	0	0	CTAGTGGCTCATTGTAAATGTGTGGTTTAACTCGT	<<<<<<<<<<0<<<<655<<7<<<:9<<3/:<6):	H0:i:1	H1:i:0	MF:i:18	NM:i:0	UQ:i:0	Aq:i:66
EAS51_64:8:5:734:57	137	seq1	5	99	35M	*	0	0	AGTGGCTCATTGTAAATGTGTGGTTTAACTCGTCC	<<<<<<<<<<<7;71<<;<;;<7;<<3;);3*8/5	H0:i:1	H1:i:0	MF:i:18	NM:i:0	UQ:i:0	Aq:i:66
B7_591:1:289:587:906	137	seq1	6	63	36M	*	0	0	GTGGCTCATTGTAATTTTTTGTTTTAACTCTTCTCT	(-&----,----)-)-),'--)---',+-,),''*,	H0:i:0	H1:i:0	MF:i:130	NM:i:5	UQ:i:38	Aq:i:63
EAS56_59:8:38:671:758	137	seq1	9	99	35M	*	0	0	GCTCATTGTAAATGTGTGGTTTAACTCGTCCATGG	<<<<<<<<<<<<<<<;<;7<<<<<<<<7<<;:<5%	H0:i:1	H1:i:0	MF:i:18	NM:i:0	UQ:i:0	Aq:i:72
EAS56_61:6:18:467:281	73	seq1	13	99	35M	*	0	0	ATTGTAAATGTGTGGTTTAACTCGTCCCTGGCCCA	<<<<<<<<;<<<8<<<<<;8:;6/686&;(16666	H0:i:0	H1:i:1	MF:i:18	NM:i:1	UQ:i:5	Aq:i:39
EAS114_28:5:296:340:699	137	seq1	13	99	36M	*	0	0	ATTGTAAATGTGTGGTTTAACTCGTCCATGGCCCAG	<<<<<;<<<;<;<<<<<<<<<<<8<8<3<8;<;<0;	H0:i:1	H1:i:0	MF:i:18	NM:i:0	UQ:i:0	Aq:i:73
B7_597:6:194:894:408	73	seq1	15	99	35M	*	0	0	TGTAAATGTGTGGTTTAACTCGTCCATTGCCCAGC	<<<<<<<<<7<<;<<<<;<<<7;;<<<*,;;572<	H0:i:0	H1:i:1	MF:i:18	NM:i:1	UQ:i:9	Aq:i:43
EAS188_4:8:12:628:973	89	seq1	18	75	35M	*	0	0	AAATGTGTGGTTTAACTCGTCCATGGCCCAGCATT	==;=:;:;;:====;=;===:=======;==;===	H0:i:1	H1:i:0	MF:i:64	NM:i:0	UQ:i:0	Aq:i:0
(...)

Bam4DeseqIntervals

creates a table for DESEQ with the number of reads within a sliding window for multiple BAMS.Version: 1.0

Compilation

```bash ant bam4deseq01 ```

Options

OptionDescription
IN=FileBAM file to process This option must be specified at least 1 times.
OUT=Fileoutput filename. Default stdout.
WINDOW_SIZE=Integersize of the observed window. Default value: 500. This option can be set to 'null' to clear the default value.
WINDOW_SHIFT=Integershift window by SHIFT pb Default value: 250. This option can be set to 'null' to clear the default value.
ONLY_COVERED=Booleanignore regions with NO coverage Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false}
HEADER=Booleanprint header Default value: true. This option can be set to 'null' to clear the default value. Possible values: {true, false}

VCFStripAnnotations

Motivation

Removes one or more field from the INFO column of a VCF.Version

Compilation

```bash ant vcfstripannot ```

Options

OptionDescription
IN=FileVCF file to process. Default stdin.
OUT=FileVCF file to generate. Default stdout. Default value: null.
KEY=Stringremove this INFO key This option may be specified 0 or more times.
RESET_FILTER=BooleanReset the FILTER column Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false}

Example

```bash $ java -jar dist/vcfstripannot.jar K=DP4 K=AC1 < in.vcf > out.vcf ```

VCFFixIndels

Motivation

Fix samtools INDELS for @SolenaLS

Compilation

```bash ant vcffixindels ```

Options

OptionDescription
IN=FileVCF file to process. Default stdin. Default value: null.
OUT=FileVCF file to generate. Default stdout. Default value: null.

Example

```bash $ java -jar dist/vcffixindels.jar I=input.vcf.gz | grep FIX

2 749862 . T TT 94.50 . AC1=2;AF1=1;DP=13;DP4=0,0,5,8;FQ=-73.5;INDEL;INDELFIXED=CTTTTTT|CTTTTTTT|74954856;IS=13,1.000000;MQ=50;VDB=4.019414e-04 GT:PL:DP:GQ 1/1:135,39,0:13:75


<h3>BlastMapAnnots</h3>
<h4>Motivation</h4>
Maps uniprot/genbank annotations on a blast result. See http://www.biostars.org/p/76056
<h4>Compilation</h4>
This tools call ${JAVA_HOME}/bin/xjc. If you're working being a proxy, you might have to edit the build.xml file to add the -httpproxy option.
```bash
ant blastmapannots

Options

OptionDescription
IN=FileXML sequence file Genbank.xml or uniprot.xml. Required.
BLAST=FileBLAST XML output (or stdin). Default value: null.
APPEND_ACN=Booleanappend the sequence accession before the feature name. Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false}
INCL=StringRestrict to uniprot/feature/type of genbank/feature/key. This option may be specified 0 or more times.
EXCL=StringExclude uniprot/feature/type of genbank/feature/key. This option may be specified 0 or more times.

Example

Download uniprot P04514 ( Rotavirus Non-structural protein 3 ) as XML ```bash $ curl -o P04514.xml "http://www.uniprot.org/uniprot/P04514.xml" ``` Download the same P04514 as fasta ```bash $ curl -o P04514.fasta "http://www.uniprot.org/uniprot/P04514.fasta" ```

TblastN P04514.fasta vs a RNA of NSP3 in genbank http://www.ncbi.nlm.nih.gov/nuccore/AY065842.1 and save the ouput as XML:

<?xml version="1.0"?>
<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">
<BlastOutput>
  <BlastOutput_program>tblastn</BlastOutput_program>
(...)
<Hit>
  <Hit_num>1</Hit_num>
  <Hit_id>gi|18139606|gb|AY065842.1|</Hit_id>
  <Hit_def>Rhesus rotavirus nonstructural protein 3 (NSP3) gene, complete cds</Hit_def>
  <Hit_accession>AY065842</Hit_accession>
  <Hit_len>1078</Hit_len>
  <Hit_hsps>
    <Hsp>
      <Hsp_bit-score>546.584</Hsp_bit-score>
      <Hsp_score>1407</Hsp_score>
      <Hsp_evalue>0</Hsp_evalue>
      <Hsp_query-from>1</Hsp_query-from>
      <Hsp_query-to>313</Hsp_query-to>
      <Hsp_hit-from>26</Hsp_hit-from>
      <Hsp_hit-to>964</Hsp_hit-to> <Hsp_qseq>MLKMESTQQMASSIINTSFEAAVVAATSTLELMGIQYDYNEIYTRVKSKFDYVMDDSGVKNNLLGKAATIDQALNGKFGSVMRNKNWMTDSRTVAKLDEDVNKLRMMLSSKGIDQKMRVLNACFSVKRIPGKSSSVIKCTRLMKDKIERGAVEVDDSFVEEKMEVDTVDWKSRYDQLERRFESLKQRVNEKYTTWVQKAKKVNENMYSLQNVISQQQNQIADLQNYCSKLEADLQNKVGSLVSSVEWYLKSMELPDEVKTDIEQQLNSIDTISPINAIDDLEILIRNLIHDYDRTFLMFKGLLRQCNYEYAYE</Hsp_qseq>
      <Hsp_hseq>MLKMESTQQMASSIINSSFEAAVVAATSTLELMGIQYDYNEVYTRVKSKFDLVMDDSGVKNNLIGKAITIDQALNGKFSSAIRNRNWMTDSRTVAKLDEDVNKLRIMLSSKGIDQKMRVLNACFSVKRIPGKSSSIVKCTRLMKDKLERGEVEVDDSFVEEKMEVDTIDWKSRYEQLEKRFESLKHRVNEKYNHWVLKARKVNENMNSLQNVISQQQAHINELQMYNNKLERDLQSKIGSVVSSIEWYLRSMELSDDVKSDIEQQLNSIDQLNPVNAIDDFESILRNLISDYDRLFIMFKGLLQQCNYTYTYE</Hsp_hseq>
      <Hsp_midline>MLKMESTQQMASSIIN SFEAAVVAATSTLELMGIQYDYNE YTRVKSKFD VMDDSGVKNNL GKA TIDQALNGKF S  RN NWMTDSRTVAKLDEDVNKLR MLSSKGIDQKMRVLNACFSVKRIPGKSSS  KCTRLMKDK ERG VEVDDSFVEEKMEVDT DWKSRY QLE RFESLK RVNEKY  WV KA KVNENM SLQNVISQQQ  I  LQ Y  KLE DLQ K GS VSS EWYL SMEL D VK DIEQQLNSID   P NAIDD E   RNLI DYDR F MFKGLL QCNY Y YE</Hsp_midline>
    </Hsp>
  </Hit_hsps>
</Hit>
(...)
</Iteration>
</BlastOutput_iterations>
</BlastOutput>

Now produce a BED file with this blast result to map the features of P04514 to AY065842.

$ java -jar dist/blastmapannots.jar I=P04514.xml B=blast.xml

AY065842	25	961	Non-structural_protein_3	943	+	25961	255,255,255	1	936	25
AY065842	34	469	RNA-binding	970	+	34	469	255,255,255	1	435	34
AY065842	472	640	Dimerization	947	+	472	640	255,255,255	1	168	472
AY065842	532	724	Interaction_with_ZC3H7B	917	+	532	724	255,255,255	1	192	532
AY065842	646	961	Interaction_with_EIF4G1	905	+	646	961	255,255,255	1	315	646
AY065842	520	733	coiled-coil_region	916	+	520	733	255,255,255	1	213	520

VcfViewGui

Motivation

Simple java-Swing-based VCF viewer. ![ScreenShot](https://raw.github.com/lindenb/jvarkit/master/doc/vcfview.png)

Compilation

```bash ant vcfviewgui ```

Options

OptionDescription
IN=FileVCF files to process. This option may be specified 0 or more times.
IGV_HOST=StringIGV host. example: '127.0.0.1' Default value: null.
IGV_PORT=IntegerIGV IP. example: '60151' Default value: null.

VCFGeneOntology

Motivation

Finds the GO terms for VCF annotated with SNPEFF or VEP

Compilation

```bash ant vcfgo ```

Options

OptionDescription
GOA=StringGOA file/URI. Default value: http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/gene-associations/gene_association.goa_human.gz?rev=HEAD.
GO=StringGOA file/URI. Default value: http://archive.geneontology.org/latest-termdb/go_daily-termdb.rdf-xml.gz.
IN=StringVCF file/URL to process. Default stdin.
OUT=FileVCF file to generate. Default stdout.

Example

```bash $ java -jar dist/vcfgo.jar I="https://raw.github.com/arq5x/gemini/master/test/tes.snpeff.vcf" |\ grep -v -E '^##' | head -n 3

#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 1094PC0005 1094PC0009 1094PC0012 1094PC0013 chr1 30860 . G C 33.46 . AC=2;AF=0.053;AN=38;BaseQRankSum=2.327;DP=49;Dels=0.00;EFF=DOWNSTREAM(MODIFIER||||85|FAM138A|protein_coding|CODING|ENST00000417324|),DOWNSTREAM(MODIFIER|||||FAM138A|processed_transcript|CODING|ENST00000461467|),DOWNSTREAM(MODIFIER|||||MIR1302-10|miRNA|NON_CODING|ENST00000408384|),INTRON(MODIFIER|||||MIR1302-10|antisense|NON_CODING|ENST00000469289|),INTRON(MODIFIER|||||MIR1302-10|antisense|NON_CODING|ENST00000473358|),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000423562|),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000430492|),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000438504|),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000488147|),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000538476|);FS=3.128;HRun=0;HaplotypeScore=0.6718;InbreedingCoeff=0.1005;MQ=36.55;MQ0=0;MQRankSum=0.217;QD=16.73;ReadPosRankSum=2.017 GT:AD:DP:GQ:PL 0/0:7,0:7:15.04:0,15,177 0/0:2,0:2:3.01:0,3,39 0/0:6,0:6:12.02:0,12,143 0/0:4,0:4:9.03:0,9,119 chr1 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;GOA=OR4F5|GO:0004984&GO:0005886&GO:0004930&GO:0016021;HRun=0;HaplotypeScore=0.0000;InbreedingCoeff=-0.0598;MQ=31.06;MQ0=0;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


<h3>VCFFilter GO</h3>
<h4>Motivation</h4>
Set the <b>VCF FILTERs</b> on VCF files annotated with SNPEFF or VCP testing wether a Gene belong or not to the descendants of a GO term. 
<h4>Compilation</h4>
```bash
ant vcffiltergo

Options

OptionDescription
CHILD_OF=Stringlist of GO accessions for gene having a GO-term children of the user output. This option may be specified 0 or more times.
FILTER=StringFilter name. Default value: GO. This option can be set to 'null' to clear the default value.
GOA=StringGOA file/URI. Default value: http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/gene-associations/gene_association.goa_human.gz?rev=HEAD. This option can be set to 'null' to clear the default value.
GO=StringGOA file/URI. Default value: http://archive.geneontology.org/latest-termdb/go_daily-termdb.rdf-xml.gz. This option can be set to 'null' to clear the default value.
IN=StringVCF file/URL to process. Default stdin.
OUT=FileVCF file to generate. Default stdout.

Example

```bash $ java -jar dist/vcffiltergo.jar I="https://raw.github.com/arq5x/gemini/master/test/test1.snpeff.vcf" \ CHILD_OF=GO:0005886 FILTER=MEMBRANE |\ grep -v "^##" | head -n 3

#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 1094PC0005 1094PC0009 1094PC0012 1094PC0013 chr1 30860 . G C 33.46 PASS AC=2;AF=0.053;AN=38;BaseQRankSum=2.327;DP=49;Dels=0.00;EFF=DOWNSTREAM(MODIFIER||||85|FAM138A|protein_coding|CODING|ENST00000417324|),DOWNSTREAM(MODIFIER|||||FAM138A|processed_transcript|CODING|ENST00000461467|),DOWNSTREAM(MODIFIER|||||MIR1302-10|miRNA|NON_CODING|ENST00000408384|),INTRON(MODIFIER|||||MIR1302-10|antisense|NON_CODING|ENST00000469289|),INTRON(MODIFIER|||||MIR1302-10|antisense|NON_CODING|ENST00000473358|),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000423562|),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000430492|),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000438504|),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000488147|),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000538476|);FS=3.128;HRun=0;HaplotypeScore=0.6718;InbreedingCoeff=0.1005;MQ=36.55;MQ0=0;MQRankSum=0.217;QD=16.73;ReadPosRankSum=2.017 GT:AD:DP:GQ:PL 0/0:7,0:7:15.04:0,15,177 0/0:2,0:2:3.01:0,3,39 0/0:6,0:6:12.02:0,12,143 0/0:4,0:4:9.03:0,9,119 chr1 69270 . A G 2694.18 MEMBRANE 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;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


<h3>VCFBed</h3>
<h4>Motivation</h4>
Annotate a VCF with the content of a BED file indexed with tabix
<h4>Compilation</h4>
```bash
ant vcfbed

Options

Option Description
FORMAT=String format. Field with ${number} will be replaced with the column of the BED. Default value: ${1}:${2}-${3}. This option can be set to 'null' to clear the default value.
TABIXFILE=String BED file indexed with tabix Required.
TAG=String Key for the INFO field Default value: TAG. This option can be set to 'null' to clear the default value.
IN=String VCF file/URL to process. Default stdin. Default value: null.
OUT=File VCF file to generate. Default stdout. Default value: null.

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  dist/vcfbed.jar TABIXFILE=~/ncbibiosystem.bed.gz TAG=NCBIBIOSYS  FMT='($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

Biostar76892

Motivation

Fix strand of two paired reads close but on the same strand http://www.biostars.org/p/76892/

Compilation

```bash ant biostar76892 ```

Options

OptionDescription
ONLYSAVEFIXED=Booleanonly save pairs of reads fixed. Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false}
DISTANCE=Integerdistance beween two reads. Default value: 500. This option can be set to 'null' to clear the default value.
IN=FileBAM file to process. Required.
OUT=FileBAM file fixed. Required.

Example

Before fixing:

samtools view src.bam | grep "HWI-1KL149:6:C0KTCACXX:5:2107:2283:35906"
HWI-1KL149:6:C0KTCACXX:5:2107:2283:35906        177     3       1264832 37      101M    =       1264940 109     AGGTGGTGAAGCATGAGATGTAGGGAGAGCTGCTTTAAAACCCAGCACAAGGCTGGTTGTACTGGCTCACACCTGTAATCCCAGGTCTTTGGGAGGCTGAG    """#""""#"""#"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""#""""""#""##"""""""#"#"   X0:i:1  X1:i:0  BD:Z:ABBACCABBABAAABABAABAACBBABAA@AAABAABBAABB@AAAAAAABA@ABAA@BAA@@BAAAAAAAA@@BAAAABA@ABAAABAACBBACBAABAA       MD:Z:0C0C0C1C0C0G1G0T1T0T0G0C0C0T0T0C0T0G0T0A0C0A2T2C0A0T0G0C1T0G0T0G2G0T0T0T0G1G0T1T1C0C0A0A0G0T0G0C0G0A1T0G1G0C0T1T0T2C0G0T0G0T0G1C1C0A1G1G0T1C0C1T0T2C0A0     RG:Z:idp63088   XG:i:0  BI:Z:ABBAEDCCCBCBBABABAAAA@CBBAB@A@@A@AAAAAAABA@@AAA@A@BA@@BAA@A@@@@BAA@A@@@A@@AAAAABA@@BAAABBACBBACBBABAA       AM:i:37 NM:i:75 SM:i:37 XM:i:1  XO:i:0  MQ:i:37 XT:A:U
HWI-1KL149:6:C0KTCACXX:5:2107:2283:35906        113     3       1264940 37      101M    =       1264832 -109    GGTATCTCCATGCTCGAAGCCCTGACCTACTGTATTGCCCCGAAAGTCTTCCCTGCTGTGGCTGCATCTTTTCCACGTGGATAATCTTGGTTCATCTCTAG    """##"""""""""""""""""""""""""#"""""""""""""""""""""""""""#"""""""""""""""#""""""""""""#""#""##"#"##"   X0:i:1  X1:i:0  BD:Z:BBAABBBBAAABBBCBAABCBA@BAAAAAAABAAAAACCCBABAAAAAAACBAAAAABABA@AA@AAABBAAAAACB@BBAAAAAAAABBBAABBBBAAAA       MD:Z:0T0T1G0C0A1G0T1C0C0A1G0T0G0C0A0T0G0T0G0T0G2A0T4G0C0A0A0T0G0T0G0C1G0G0T0G1C0A0G0T0T0G0C0A4C1A0T0G0C0G0T0G2G0G1C0G0T0G0A1C0G0T0G1G0C2T2T0C0G0T0G0T0A0T1       RG:Z:idp63088   XG:i:0  BI:Z:BABADDCCBBBCBBCBAABCBA@AABAAA@AAAAA@BBBBBAAA@AA@AABA@@A@@A@BA@@A@AA@AAAAAAABB@BAAAAAAAA@CBAAABBBBAAAA       AM:i:37 NM:i:74 SM:i:37 XM:i:0  XO:i:0  MQ:i:37 XT:A:U

Fixing:

 java -jar dist/biostar76892.jar ONLYSAVEFIXED=true \
 	IN=src.bam \
 	OUT=fix.bam  \
 	VALIDATION_STRINGENCY=LENIENT

result

samtools view fix.bam | grep "HWI-1KL149:6:C0KTCACXX:5:2107:2283:35906"
HWI-1KL149:6:C0KTCACXX:5:2107:2283:35906        163     3       1264832 37      101M    =       1264940 109     AGGTGGTGAAGCATGAGATGTAGGGAGAGCTGCTTTAAAACCCAGCACAAGGCTGGTTGTACTGGCTCACACCTGTAATCCCAGGTCTTTGGGAGGCTGAG    """#""""#"""#"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""#""""""#""##"""""""#"#"   X0:i:1  X1:i:0  BD:Z:ABBACCABBABAAABABAABAACBBABAA@AAABAABBAABB@AAAAAAABA@ABAA@BAA@@BAAAAAAAA@@BAAAABA@ABAAABAACBBACBAABAA       MD:Z:0C0C0C1C0C0G1G0T1T0T0G0C0C0T0T0C0T0G0T0A0C0A2T2C0A0T0G0C1T0G0T0G2G0T0T0T0G1G0T1T1C0C0A0A0G0T0G0C0G0A1T0G1G0C0T1T0T2C0G0T0G0T0G1C1C0A1G1G0T1C0C1T0T2C0A0     RG:Z:idp63088   XG:i:0  BI:Z:ABBAEDCCCBCBBABABAAAA@CBBAB@A@@A@AAAAAAABA@@AAA@A@BA@@BAA@A@@@@BAA@A@@@A@@AAAAABA@@BAAABBACBBACBBABAA       AM:i:37 NM:i:75 SM:i:37 XM:i:1  XO:i:0  MQ:i:37 XT:A:U  rv:i:1
HWI-1KL149:6:C0KTCACXX:5:2107:2283:35906        83      3       1264940 37      101M    =       1264832 -109    GGTATCTCCATGCTCGAAGCCCTGACCTACTGTATTGCCCCGAAAGTCTTCCCTGCTGTGGCTGCATCTTTTCCACGTGGATAATCTTGGTTCATCTCTAG    """##"""""""""""""""""""""""""#"""""""""""""""""""""""""""#"""""""""""""""#""""""""""""#""#""##"#"##"   X0:i:1  X1:i:0  BD:Z:BBAABBBBAAABBBCBAABCBA@BAAAAAAABAAAAACCCBABAAAAAAACBAAAAABABA@AA@AAABBAAAAACB@BBAAAAAAAABBBAABBBBAAAA       MD:Z:0T0T1G0C0A1G0T1C0C0A1G0T0G0C0A0T0G0T0G0T0G2A0T4G0C0A0A0T0G0T0G0C1G0G0T0G1C0A0G0T0T0G0C0A4C1A0T0G0C0G0T0G2G0G1C0G0T0G0A1C0G0T0G1G0C2T2T0C0G0T0G0T0A0T1       RG:Z:idp63088   XG:i:0  BI:Z:BABADDCCBBBCBBCBAABCBA@AABAAA@AAAAA@BBBBBAAA@AA@AABA@@A@@A@BA@@A@AA@AAAAAAABB@BAAAAAAAA@CBAAABBBBAAAA       AM:i:37 NM:i:74 SM:i:37 XM:i:0  XO:i:0  MQ:i:37 XT:A:U  rv:i:1

FixVCF

Motivation

Fix a VCF HEADER when I forget to declare a FILTER or an INFO field in the HEADER

Compilation

```bash ant fixvcf ```

Options

OptionDescription
IN=StringVCF file/URL to process. Default stdin.
OUT=FileVCF file to generate. Default stdout.

VCFTrio

Motivation

Check for mendelian incompatibilities in a VCF

Compilation

```bash ant vcftrio ```

Options

OptionDescription
PEDIGREE=File Pedigree file (plink format) Required.
FILTER=BooleanSet filter 'MENDEL' if incompatibilities found. Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false}
IN=StringVCF file/URL to process. Default stdin. Default value: null.
OUT=FileVCF file to generate. Default stdout. Default value: null.

MapUniProtFeatures

Motivation

map uniprot features on reference genome.

Options

OptionDescription
REF=FileReference Required.
OUT=Fileoutput name (default: stdout) Required.
KGURI=StringKnownGene data Default value: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/knownGene.txt.gz. This option can be set to 'null' to clear the default value.
UNIPROT=StringUniprot URL/File Default value: ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.xml.gz. This option can be set to 'null' to clear the default value.

Example

```bash $ java -jar dist/mapuniprot.jar \ REF=/path/to/human_g1k_v37.fasta \ UNIPROT=/path/uri/uniprot.org/uniprot_sprot.xml.gz \ kgUri=<(curl -s "http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/knownGene.txt.gz" | gunzip -c | awk -F ' ' '{if($2 ~ ".*_.*") next; OFS=" "; gsub(/chr/,"",$2);print;}' ) |\ LC_ALL=C sort -t ' ' -k1,1 -k2,2n -k3,3n | uniq | head

1 69090 69144 topological_domain 1000 + 69090 69144 255,0,0 1 54 0 1 69144 69216 transmembrane_region 1000 + 69144 69216 255,0,0 1 72 0 1 69216 69240 topological_domain 1000 + 69216 69240 255,0,0 1 24 0 1 69240 69306 transmembrane_region 1000 + 69240 69306 255,0,0 1 66 0 1 69306 69369 topological_domain 1000 + 69306 69369 255,0,0 1 63 0 1 69357 69636 disulfide_bond 1000 + 69357 69636 255,0,0 1 279 0 1 69369 69429 transmembrane_region 1000 + 69369 69429 255,0,0 1 60 0 1 69429 69486 topological_domain 1000 + 69429 69486 255,0,0 1 57 0 1 69486 69543 transmembrane_region 1000 + 69486 69543 255,0,0 1 57 0 1 69543 69654 topological_domain 1000 + 69543 69654 255,0,0 1 111 0

<h3>ExtendBed</h3>
<h4>Motivation</h4>
Extends a BED file by 'X' bases.
<h4>Options</h4>
<table>
<tr><th>Option</th><th>Description</th></tr>
<tr><td>IN=String</td><td>BED Input URI/file. default: stdin  Default value: null. </td></tr>
<tr><td>REF=File</td><td>Reference  Required. </td></tr>
<tr><td>OUT=File</td><td>output name (default: stdout)</td></tr>
<tr><td>EXTEND=Integer</td><td>extend by 'X' bases.  Default value: 0. This option can be set to 'null' to clear the default value. </td></tr>
</table>
<h4>Example</h4>
```bash
head test.bed |\
	java -jar dist/extendbed.jar \
	X=100 REF=human_g1k_v37.fa

Biostar77288

Motivation

Low resolution sequence alignment visualization http://www.biostars.org/p/77288/

Compilation

```bash ant biostar77288 ```

Options

OptionDescription
IN=StringMSA file/URI (default:stdin)
ALN_WIDTH=IntegerAlignment width Default value: 1000. This option can be set to 'null' to clear the default value.
SEQLOGO=BooleanInput is seqLogo (see https://github.com/lindenb/jvarkit#sam4weblogo) Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false}

Example

```bash curl -s "http://www.tcoffee.org/Courses/Exercises/saragosa_pb_2010/practicals/practical_2/ex.1.19/file/clustalw.msa" |\ java -jar dist/biostar77288.jar > result.svg ``` ![ScreenShot](https://raw.github.com/lindenb/jvarkit/master/doc/biostar77288.png) ```bash $ java -jar dist/sam4weblogo.jar IN=in.bam REGION="1:630-719" |\ java -jar dist/biostar77288.jar SEQLOGO=true > result.svg ```

VCFAnnotator

Motivation

Basic Variant Effect prediction . First described in http://plindenbaum.blogspot.fr/2011/01/my-tool-to-annotate-vcf-files.html

Compilation

```bash ant vcfpredictions ```

Options

OptionDescription
REF=Fileindexed Fasta genome REFERENCE. Required.
KGURI=StringKnownGene data URI/File. should look like http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/knownGene.txt.gz . Beware chromosome names are formatted the same as your REFERENCE. Default value: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/knownGene.txt.gz. This option can be set to 'null' to clear the default value.
IN=StringVCF file/URL to process. Default stdin. Default value: null.
OUT=FileVCF file to generate. Default stdout. Default value: null.

Example

```bash java -jar dist/vcfpredictions.jar \ REF=human_g1k_v37.fasta \ kgUri=<(curl "http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/knownGene.txt.gz" | gunzip -c | awk -F ' ' '{if($2 ~ ".*_.*") next; OFS=" "; gsub(/chr/,"",$2);print;}' ) \ I=~/WORK/variations.gatk.annotations.vcf.gz ```

VCFBigWig

Motivation

Annotate a VCF with the data of a bigwig file.

Compilation

Compiling requires the bigwig library http://code.google.com/p/bigwig/ 
$ more build.properties 
(...)
bigwig.dir=/path/to/bigwig
(...)

$ ant vcfbigwig

Options

OptionDescription
BW=File Path to the bigwig file. The chromosome must have the same names than in the VCF. Required.
INFOTAG=Stringname of the INFO tag. default: name of the bigwig. Default value: null
IN=StringVCF file/URL to process. Default stdin. Default value: null.
OUT=FileVCF file to generate. Default stdout. Default value: null.

Example

```bash java -jar dist/vcfbigwig.jar \ IN=input.vcf.gz \ INFOTAG=GERP \ BW=gerp.bw

##INFO=<ID=GERP,Number=1,Type=Float,Description="Values from bigwig file: com.github.lindenb.jvarkit.tools.vcfbigwig.VCFBigWig BIGWIG=gerp.bw TAG=GERP IN=input.vcf.gz VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false"> #CHROM POS ID REF ALT QUAL FILTER INFO(...) A 33926 . G A 182 . GERP=-6.35(...) A 45365 . A G 222 . GERP=-3.55(...)


<h3>VCFTabixml</h3>
<h4>Motivation</h4>
Annotate a value from a vcf+xml file.4th column of the BED indexed with TABIX is a XML string.It will be processed with the xslt-stylesheet and should procuce a xml result &lt;properties>&lt;property key='key1'>value1&lt;/property>&lt;property key='key2'>values1&lt;/property>&lt;/properies> INFO fields. Carriage returns will be removed.Parameters to be passed to the stylesheet: vcfchrom (string) vcfpos(int) vcfref(string) vcfalt(string). Version: 1.0
<h4>Compilation</h4>
```bash
ant vcftabixml

Options

OptionDescription
BEDFILE=String BED file indexed with tabix. The 4th column *is* a XML string.) Required.
STYLESHEET=Filex xslt-stylesheet. REQUIRED. Should produce a valid set of INFO field. Required.
TAGS=Filefile containing extra INFO headers line to add version: 4.1 Required.
IN=StringVCF file/URL to process. Default stdin. Default value: null.
OUT=FileVCF file to generate. Default stdout. Default value: null.

Example

The header of the tabix-index BED+XML file: ``` 1 69427 69428 1:6942869428G/T1:6947669476C/T1:6949669496A/G1:6951169511G/A1:6959069590A/T1:6959469594C/T1:6962069620T/TA1:6974569745CA/C1:6976169761T/A1:801943801943T/C ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ``` The XSLT file: 
<?xml version="1.0" encoding="ISO-8859-1"?>
<xsl:stylesheet xmlns:xsl="http://www.w3.org/1999/XSL/Transform" version="1.0"> 
<xsl:output method="xml"/>
<xsl:param name="vcfchrom"/>
<xsl:param name="vcfpos"/>
<xsl:param name="vcfref"/>
<xsl:param name="vcfalt"/>
<xsl:template match="/">
<properties>
<xsl:apply-templates select="evsData|snpList"/>
</properties>
</xsl:template>
<xsl:template match="evsData">
<xsl:apply-templates select="snpList"/>
</xsl:template>
<xsl:template match="snpList">
<xsl:choose>
 <xsl:when test="chromosome=$vcfchrom and chrPosition=$vcfpos and refAllele=$vcfref">
<xsl:apply-templates select="clinicalLink|rsIds|uaMAF|aaMAF|totalMAF|avgSampleReadDepth|geneList|conservationScore|conservationScoreGERP|gwasPubmedIds|onExomeChip|gwasPubmedIds"/>
  <xsl:if test="altAlleles!=$vcfalt">
  	<property key="EVS_CONFLICTALT">
  		<xsl:value-of select="altAlleles"/>
  	</property>		
  	</xsl:if>
  </xsl:when>
  <xsl:otherwise/>
</xsl:choose>
</xsl:template>
<xsl:template match="clinicalLink|rsIds|uaMAF|aaMAF|totalMAF|avgSampleReadDepth|geneList|conservationScore|conservationScoreGERP|onExomeChip|gwasPubmedIds">
<xsl:if test="string-length(normalize-space(text()))&gt;0">
<property>
<xsl:attribute name="key"><xsl:value-of select="concat('EVS_',translate(name(.),'abcdefghijklmnopqrstuvwxyz','ABCDEFGHIJKLMNOPQRSTUVWXYZ'))"/></xsl:attribute>
<xsl:value-of select="text()"/>
</property>
</xsl:if>
</xsl:template>
</xsl:stylesheet>

Running:

java -jar dist/vcftabixml.jar \
	IN=input.vcf.gz \
	XSL=evs2vcf.xsl \
	BEDFILE=evs.data.gz \
	TAGS=tags.txt | grep -v "##" | head

#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	U0925
A	613326	.	G	A	182	.	AC1=1;AF1=0.5;DP=327;DP4=0,147,0,178;FQ=163;MQ=47;PV4=1,0.21,1.2e-35,1;RPB=6.999638e+00;VDB=8.105711e-05	GT:PL:DP:GQ	0/1:212,0,190:325:99
A	614565	.	A	G	222	.	AC1=2;AF1=1;DP=910;DP4=0,1,71,836;EVS_AAMAF=23.2659;EVS_AVGSAMPLEREADDEPTH=70;EVS_CLINICALLINK=unknown;EVS_CONSERVATIONSCORE=0.0;EVS_CONSERVATIONSCOREGERP=-3.5;EVS_GENELIST=KCNAB2;EVS_GWASPUBMEDIDS=unknown;EVS_ONEXOMECHIP=false;EVS_RSIDS=rs26;EVS_TOTALMAF=30.5519;EVS_UAMAF=33.7209;FQ=-282;MQ=41;PV4=1,0.26,0.032,1;RPB=1.705346e+00;VDB=1.656917e-35	GT:PL:DP:GQ	1/1:255,255,0:908:99
A	614379	.	C	T	225	.	AC1=1;AF1=0.5;DP=979;DP4=33,440,37,456;EVS_AAMAF=2.8179;EVS_AVGSAMPLEREADDEPTH=59;EVS_CLINICALLINK=unknown;EVS_CONSERVATIONSCORE=0.0;EVS_CONSERVATIONSCOREGERP=-4.7;EVS_GENELIST=KCNAB2;EVS_GWASPUBMEDIDS=unknown;EVS_ONEXOMECHIP=false;EVS_RSIDS=rs249;EVS_TOTALMAF=8.8261;EVS_UAMAF=11.4393;FQ=225;MQ=42;PV4=0.8,1,3.8e-152,1;RPB=1.317662e+01;VDB=3.857882e-21	GT:PL:DP:GQ	0/1:255,0,255:966:99
A	614565	.	T	G	222	.	AC1=2;AF1=1;DP=209;DP4=0,0,0,187;FQ=-282;MQ=46;VDB=2.410569e-12	GT:PL:DP:GQ	1/1:255,255,0:187:99
A	614953	.	C	T	225	.	AC1=1;AF1=0.5;DP=810;DP4=197,214,194,195;EVS_AAMAF=2.4603;EVS_AVGSAMPLEREADDEPTH=45;EVS_CLINICALLINK=unknown;EVS_CONSERVATIONSCORE=0.0;EVS_CONSERVATIONSCOREGERP=-3.1;EVS_GENELIST=KCNAB2;EVS_GWASPUBMEDIDS=unknown;EVS_ONEXOMECHIP=false;EVS_RSIDS=rs733;EVS_TOTALMAF=7.0506;EVS_UAMAF=9.4205;FQ=225;MQ=47;PV4=0.62,1,9.2e-58,0.015;RPB=4.560133e+00;VDB=6.880316e-03	GT:PL:DP:GQ	0/1:255,0,255:800:99
A	614922	.	G	A	130	.	AC1=1;AF1=0.5;DP=183;DP4=0,94,0,86;EVS_AAMAF=2.3053;EVS_AVGSAMPLEREADDEPTH=43;EVS_CLINICALLINK=unknown;EVS_CONSERVATIONSCORE=0.0;EVS_CONSERVATIONSCOREGERP=-3.0;EVS_GENELIST=KCNAB2;EVS_GWASPUBMEDIDS=unknown;EVS_ONEXOMECHIP=false;EVS_RSIDS=rs202;EVS_TOTALMAF=7.1215;EVS_UAMAF=9.6386;FQ=133;MQ=44;PV4=1,0.0065,3.7e-51,1;RPB=3.500959e+00;VDB=9.915205e-29	GT:PL:DP:GQ	0/1:160,0,184:180:99
A	614986	.	G	C	188	.	AC1=2;AF1=1;DP=176;DP4=0,0,0,175;FQ=-282;MQ=46;VDB=0.000000e+00	GT:PL:DP:GQ	1/1:221,255,0:175:99
A	615009	.	T	A	125	.	AC1=1;AF1=0.5;DP=103;DP4=45,0,56,0;FQ=120;MQ=45;PV4=1,0.14,2.8e-19,1;RPB=1.520268e+00;VDB=1.539079e-06	GT:PL:DP:GQ	0/1:155,0,148:101:99
A	615037	.	C	T	161	.	AC1=1;AF1=0.5;DP=353;DP4=0,164,0,165;FQ=110;MQ=48;PV4=1,1,1.1e-23,1;RPB=5.549816e+00;VDB=1.486773e-11	GT:PL:DP:GQ	0/1:191,0,137:329:99

SplitBam

####Motivation

Split a BAM by chromosome group. Create EMPTY bams if no reads was found for a given group.

####Compilation

ant splitbam

Options

OptionDescription
REF=FileIndexex reference Required.
IN=FileBAM file to process. Default stdin. Default value: null.
GENERATE_EMPTY_BAM=Booleangenerate EMPTY bams for chromosome having no read mapped. Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false}
CHROM_GROUP=FileChromosome group file. Default value: null.
ADD_MOCK_RECORD=Booleanadd a mock pair of sam records to the bam. Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false}
OUT_FILE_PATTERN=StringMUST contain __CHROM__ and end with .bam. Default value: . This option can be set to 'null' to clear the default value.
UNDERTERMINED_NAME=StringUnmapped chromosome name. Default value: Unmapped. This option can be set to 'null' to clear the default value.
INPUT_IS_SORTED=Booleaninput is sorted. Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false}

Example

the content of 'split_g1k_v37_01.txt'

CHROMS_01_09	1 2 3 4 5 6 7 8 9
CHROMS_10_0Y	10 11 12 13 14 15 16 17 18 19 20 21 22 X Y 
CHROMS_OTHER	MT GL000207.1 GL000226.1 GL000229.1 GL000231.1 GL000210.1 GL000239.1 GL000235.1 GL000201.1 GL000247.1 GL000245.1 GL000197.1 GL000203.1 GL000246.1 GL000249.1 GL000196.1 GL000248.1 GL000244.1 GL000238.1 GL000202.1 GL000234.1 GL000232.1 GL000206.1 GL000240.1 GL000236.1 GL000241.1 GL000243.1 GL000242.1 GL000230.1 GL000237.1 GL000233.1 GL000204.1 GL000198.1 GL000208.1 GL000191.1 GL000227.1 GL000228.1 GL000214.1 GL000221.1 GL000209.1 GL000218.1 GL000220.1 GL000213.1 GL000211.1 GL000199.1 GL000217.1 GL000216.1 GL000215.1 GL000205.1 GL000219.1 GL000224.1 GL000223.1 GL000195.1 GL000212.1 GL000222.1 GL000200.1 GL000193.1 GL000194.1 GL000225.1 GL000192.1

split the output of bwa sampe on the fly:

bwa sampe (...) |\
java -jar dist/splitbam.jar \
	VALIDATION_STRINGENCY=LENIENT  \
	OUT_FILE_PATTERN=TESTSPLITBAM/__CHROM__.bam \
	REF=human_g1k_v37.fasta \
	ADD_MOCK_RECORD=true \
	GENERATE_EMPTY_BAM=true \
	GP=split_g1k_v37_01.txt 


[Fri Jul 26 13:25:56 CEST 2013] Executing as lindenb@master on Linux 2.6.32-358.6.2.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_19-mockbuild_2013_04_17_19_18-b00; Picard version: null
INFO	2013-07-26 13:25:56	SplitBam	reading stdin
INFO	2013-07-26 13:25:56	SplitBam	opening TESTSPLITBAM/CHROMS_01_09.bam
INFO	2013-07-26 13:25:57	SplitBam	opening TESTSPLITBAM/CHROMS_10_0Y.bam
INFO	2013-07-26 13:25:58	SplitBam	opening TESTSPLITBAM/CHROMS_OTHER.bam
INFO	2013-07-26 13:35:58	SplitBam	closing group CHROMS_01_09
INFO	2013-07-26 13:35:59	SplitBam	closing group CHROMS_10_0Y
INFO	2013-07-26 13:35:59	SplitBam	closing group CHROMS_OTHER
INFO	2013-07-26 13:36:00	SplitBam	closing group Unmapped
Runtime.totalMemory()=1916600320

FindCorruptedFiles

Motivation

Searches for corrupted NGS files (VCF/BAM/FASTQ).

When a parallel workflow/Makefile/cluster/qmake fails, some files may be truncated, this tool will detect the files having a problem.

Compilation

ant findcorruptedfiles

Options

OptionDescription
IN=FileFile(s) and/or directories This option may be specified 0 or more times.
NUM=Longnumber of features (sam-record, variant, fastq) to read. -1= read everything. Default value: 100. This option can be set to 'null' to clear the default value.

Example

java -jar dist/findcorruptedfiles.jar \
	I=path1 \
	I=path/to/dir2 \
	VALIDATION_STRINGENCY=SILENT 2> /dev/null

NgsFilesSummary

Motivation

Scan folders and generate a summary of the files (SAMPLE/BAM SAMPLE/VCF etc..)

Compilation

ant ngsfilessummary

Options

OptionDescription
IN=FileFile(s) and/or directories This option may be specified 0 or more times.

Example

java -jar dist/ngsfilessummary.jar \
	I=/projects/align01/ \
	VALIDATION_STRINGENCY=SILENT 2> /dev/null

SAMPLE1	BAM	/projects/align01/Samples/SAMPLE1/BAM/SAMPLE1_final.bam	321262321	Wed Jun 26 10:30:07 CEST 2013
SAMPLE1	FASTQ	/projects/data
SAMPLE1	VCF	/projects/align01/Samples/SAMPLE1/VCF/SAMPLE1_variations.freebayes.vcf.gz	184191	Mon Jun 17 14:47:22 CEST 2013
SAMPLE1	VCF	/projects/align01/Samples/SAMPLE1/VCF/SAMPLE1_variations.gatk.vcf.gz	113341	Mon Jun 17 11:57:19 CEST 2013
SAMPLE1	VCF	/projects/align01/Samples/SAMPLE1/VCF/SAMPLE1_variations.samtools.vcf.gz	57518	Mon Jun 17 11:58:49 CEST 2013
SAMPLE2	BAM	/projects/align01/Samples/SAMPLE2/BAM/SAMPLE2_final.bam	286100773	Wed Jun 26 10:47:09 CEST 2013
SAMPLE2	FASTQ	/projects/data
SAMPLE2	VCF	/projects/align01/Samples/SAMPLE2/VCF/SAMPLE2_variations.freebayes.vcf.gz	172970	Mon Jun 17 14:45:51 CEST 2013
SAMPLE2	VCF	/projects/align01/Samples/SAMPLE2/VCF/SAMPLE2_variations.gatk.vcf.gz	106390	Mon Jun 17 11:57:19 CEST 2013
SAMPLE2	VCF	/projects/align01/Samples/SAMPLE2/VCF/SAMPLE2_variations.samtools.vcf.gz	52709	Mon Jun 17 11:58:04 CEST 2013

Biostar77828

Motivation

Divide the human genome among X cores, taking into account gaps See http://www.biostars.org/p/77828/

Compilation

ant biostar77828

Options

OptionDescription
IN=FileBed file input (default stdin) Default value: null.
MIN_CORE=Integermin_core Default value: 20. This option can be set to 'null' to clear the default value.
MAX_CORE=Integermax_core Default value: 30. This option can be set to 'null' to clear the default value.
N_ITERATIONS=Longnumber of iterations Default value: 1000000. This option can be set to 'null' to clear the default value.

Biostar78285

Motivation

Extract regions of genome that have 0 coverage See http://www.biostars.org/p/78285/

Compilation

ant biostar78285

Options

OptionDescription
IN=FileBAM file (sorted on coordinate). Default:stdin Default value: null.
USECIGAR=Booleanscan the CIGAR string & detect the gaps in the reads. Slower & requires more memory Default value: false.

Example:

 $ java -jar dist/biostar78285.jar \
 	I=sorted.bam \
 	USECIGAR=false \
 	VALIDATION_STRINGENCY=LENIENT

seq1	1569	1575
seq2	1567	1584

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Java utilities for NGS

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