VCFFixIndels

##Motivation

Fix samtools indels (for @SolenaLS)

##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 vcffixindels

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 vcffixindels 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/vcffixindels.jar  [options] (stdin|file.vcf|file.vcf.gz) 

Options

• -o|--output (OUTPUT-FILE) Output file. Default:stdout
• -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/vcffixindels/VCFFixIndels.java

See also

• https://github.com/lindenb/jvarkit/wiki/VCFFixIndels
• "Unified Representation of Genetic Variants" http://bioinformatics.oxfordjournals.org/content/early/2015/02/19/bioinformatics.btv112.abstract (hey ! it was published after I wrote this tool !)
• https://github.com/quinlan-lab/vcftidy/blob/master/vcftidy.py
• http://www.cureffi.org/2014/04/24/converting-genetic-variants-to-their-minimal-representation/

Example

$ curl -s "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/supporting/input_callsets/si/ALL.wgs.samtools_pass_filter.20130502.snps_indels.low_coverage.sites.vcf.gz" |\
 gunzip -c | java -jar dist/vcfstripannot.jar -k '*' 2> /dev/null |\
 java -jar dist/vcffixindels.jar  2> /dev/null | grep FIX | head -n 15

##INFO=<ID=INDELFIXED,Number=1,Type=String,Description="Fix Indels for @SolenaLS (position|alleles...)">
1   2030133 .   T   TTTTGT,TTTTG    999 PASS    INDELFIXED=2030101|CGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGT*|CGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGT|CGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTG
1   3046430 .   C   CCCT,CCC    999 PASS    INDELFIXED=3046429|TC*|TCCCT|TCCC
1   4258325 rs137902679;rs61115653  A   AAT,AA  999 PASS    INDELFIXED=4258316|CAAAAAAAAA*|CAAAAAAAAAA|CAAAAAAAAAAT
1   5374885 rs59294415  C   CCCC,CCCCA  999 PASS    INDELFIXED=5374881|TCCCC*|TCCCCCCC|TCCCCCCCA
1   5669438 rs143435517 C   CACAT,CAC   999 PASS    INDELFIXED=5669414|TACACACACACACACACACACACAC*|TACACACACACACACACACACACACAC|TACACACACACACACACACACACACACAT
1   5702062 .   A   AA,AAC  999 PASS    INDELFIXED=5702060|TAA*|TAAAC|TAAA
1   5713682 rs70977965  A   AAAAA,AAAAAC    999 PASS    INDELFIXED=5713678|CAAAA*|CAAAAAAAA|CAAAAAAAAC
1   5911136 .   T   TGCCATT,TGCCATTCCAAAGAGGCACTCA  999 PASS    INDELFIXED=5911135|CT*|CTGCCATTCCAAAGAGGCACTCA|CTGCCATT
1   6067269 rs34064079;rs59468731   G   GG,GGC  999 PASS    INDELFIXED=6067261|TGGGGGGGG*|TGGGGGGGGG|TGGGGGGGGGC
1   6069948 .   TC  T,TTC   999 PASS    INDELFIXED=6069933|CTTTTTTTTTTTTTTTC*|CTTTTTTTTTTTTTTTTC|CTTTTTTTTTTTTTTT
1   6480784 .   C   CGGGCCCCAGGCTGCCCGCC,CGGGCCCCAGGCTGCCCGCCT  999 PASS    INDELFIXED=6480783|GC*|GCGGGCCCCAGGCTGCCCGCCT|GCGGGCCCCAGGCTGCCCGCC
1   6829081 rs34184977;rs5772255    A   AAC,AA  999 PASS    INDELFIXED=6829070|TAAAAAAAAAAA*|TAAAAAAAAAAAA|TAAAAAAAAAAAAC
1   7086193 .   AG  A,AAG   999 PASS    INDELFIXED=7086179|TAAAAAAAAAAAAAAG*|TAAAAAAAAAAAAAAAG|TAAAAAAAAAAAAAA
1   8096161 .   T   TATATATATAC,TAT 999 PASS    INDELFIXED=8096143|CATATATATATATATATAT*|CATATATATATATATATATAT|CATATATATATATATATATATATATATAC

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

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