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size of indels called by UnifiedGenotyper

dghodgho Posts: 4Member
edited February 18 in Ask the GATK team

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

Post edited by dgho on

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