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Created 2012-07-23 23:55:58 | Updated 2012-07-23 23:55:58 | Tags: insertsizedistribution gatkdocs
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A new tool has been released!

Check out the documentation at InsertSizeDistribution.

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Created 2014-02-18 19:05:14 | Updated 2014-02-18 19:06:52 | Tags: unifiedgenotyper insertsizedistribution indels
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Hi, I have run gatk UnifiedGenotyper on ~45 human whole exomes. I have noticed that the maximum size for called indels in these exomes is 60bp. My question is, is 60 a default for the maximum indel size? I can't seem to find information regarding the threshold for indel size called by UnifiedGenotyper. Is the maximum indel size a parameter that can be adjusted?

In case this is of any use; This is the command I am using:

java -jar /usr/local/gatk/2.6-4/GenomeAnalysisTK.jar -R Homo_sapiens_assembly19.fasta -T UnifiedGenotyper -glm INDEL -I bams.list -L Targets.bed -stand_call_conf 30.0 -stand_emit_conf 10.0 -dcov 1000

Thank you very much for your support! Dalia