Update docs with note about SnpEff arguments.

churchlab · Jul 5, 2017 · 423b000 · 423b000
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diff --git a/docs/technical_details/snv_calling.rst b/docs/technical_details/snv_calling.rst
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 **************************
 SNV Calling and Annotation
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+SNV calling is performed by Freebayes.
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+Annotation of variants is performed by SnpEff. The default arguments to SnpEff are specified in the code `here <https://github.com/churchlab/millstone/blob/972cf2e7c38d796ec49aebb77a1aec5742986f13/genome_designer/pipeline/variant_effects.py#L320>`_ and some can be overriden by modifying local_settings.py and restarting the Millstone web server and celery.