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mkatari-bioinformatics-august-2013-gatknotes [2014/10/09 13:12] – mkatarimkatari-bioinformatics-august-2013-gatknotes [2015/06/08 07:45] – mkatari
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     -o namikonga_albert_filter.vcf \     -o namikonga_albert_filter.vcf \
     --variant /home/emasumba/Namikonga_Albert.gatk.vcf \     --variant /home/emasumba/Namikonga_Albert.gatk.vcf \
-    --filterExpression "QD < 2.0 || MQ < 40.0 || FS > 60.0 || HaplotypeScore >13.0" --filterName "mannyfilter"+    --filterExpression "QD < 2.0 || MQ < 40.0 || FS > 60.0 || HaplotypeScore >13.0" \ 
 +    --filterName "mannyfilter"
  
 </code> </code>
 +
 +Good descriptions of the different information on vcf files [[https://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_gatk_tools_walkers_annotator_HaplotypeScore.php|GATK Docs]]
  
 Finally to save the SNPs that passed your filter, you simply use the selectvariant tool. Finally to save the SNPs that passed your filter, you simply use the selectvariant tool.
mkatari-bioinformatics-august-2013-gatknotes.txt · Last modified: 2016/08/17 08:37 by mkatari