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How to select variants that have multiple alleles with JEXL

thondeboerthondeboer Redwood City, CA, USAMember ✭✭

I am trying to select variant sites that have more than one alternative allele.
How do I construct a JEXl expression to select those sites?

I suspect there is a VC field I can use but I cannot find any description of the possible variant context functions that are supported.



Best Answer


  • pdexheimerpdexheimer Member ✭✭✭✭

    Related to this, where did VariantContext go in the codebase? It looks like it's now in org.broadinstitute.variant, but I can't find that package in the source anymore. If the source is no longer available, can I request (another) documentation feature - publish the API out of it?

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    The Variant package has been transferred to the care of the Picard team, who provide their sources via sourceforge.

    The picard-public repository on sourceforge, in addition to housing the sam-jdk and picard-public, is now home to tribble and the org.broadinstitute.variant package (which includes VariantContext and associated classes as well as the VCF/BCF codecs).

    The command to check out the sources is :

    svn checkout svn://svn.code.sf.net/p/picard/code/trunk picard-public
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