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Select indels with lenght smaller than 10.

WimSWimS Member Posts: 27

How can I select indels with lenght smaller than 10 bp from a vcf file?

I tried

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.

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