-
Notifications
You must be signed in to change notification settings - Fork 133
VCFFixIndels
Pierre Lindenbaum edited this page Mar 24, 2015
·
16 revisions
Fix samtools INDELS for @SolenaLS
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. |
$ java -jar dist/vcffixindels.jar 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
- "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
- 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.