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VCFFixIndels
Pierre Lindenbaum edited this page Mar 24, 2015
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Fix variants Alleles in VCF (for @SolenaLS) Works with multiple allele in the ALT column
See also Compilation
$ make vcffixindels| Option | Description |
|---|---|
| -o (filename) | filename out. Default: stdout |
| -h | get help (this screen) and exit. |
| -v | print version and exit. |
| -L (level) | log level. One of java.util.logging.Level . Optional. |
$ 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
##Source Code
Main code is: https://github.com/lindenb/jvarkit/blob/master/src/main/java/com/github/lindenb/jvarkit/tools/vcffixindels/VCFFixIndels.java
- "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/
- Issue Tracker: http://github.com/lindenb/jvarkit/issues`
- Source Code: http://github.com/lindenb/jvarkit
##History
- 2013 : Creation
The project is licensed under the MIT license.