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Question: SelectVariants and JEXL
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gravatar for petersam
2.5 years ago by
petersam • 0
petersam • 0 wrote:

Thank you for your help. I have a vcf file which is composed of 8 samples. I would like to us SelectVariants to get a vcf list of locations where sample1 is homologous alt or hetrozygous. I attempt to use vc.getGenotype("Sample1").isHet or variations around that but am having difficulty having the JEXL expression recognized. Any advice?
selectvariants jexl gatk • 694 views
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modified 2.5 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.5 years ago by petersam • 0
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gravatar for Jennifer Hillman Jackson
2.5 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

I think that you just need to enter the term for the search in the tool form box. For example:

isHet == 1

See item 4 here for the query structure rules: http://gatkforums.broadinstitute.org/gatk/discussion/1255/using-jexl-to-apply-hard-filters-or-select-variants-based-on-annotation-values

Please give this a try. Jen, Galaxy team
ADD COMMENT • link written 2.5 years ago by Jennifer Hillman Jackson ♦ 25k
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