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How can I select indels with lenght smaller than 10 bp from a vcf file?
java -jar GenomeAnalysisTK.jar -T SelectVariants -R ref.fa --variant INDEL.vcf -o INDEL_maxLenght10.vcf -select 'vc.getIndelLengths().0 < 10'
but the output still contains all the Indels, also the ones larger than 10 bp.