Explain keep_duplicates and keep_multimappers.

bcbio · Oct 18, 2019 · 16d9ea6 · 16d9ea6
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diff --git a/docs/contents/configuration.rst b/docs/contents/configuration.rst
@@ -1053,6 +1053,8 @@ ChIP/ATAC sequencing
 - ``antibody``: automatically sets peakcalling options tailored for the specific anitbody. Supports
 `h3f3a`, `h3k27me3`, `h3k36me3`, `h3k4me1`, `h3k79me2`, `h3k9me3`, `h3k9me1`, `h3k9me2`, `h4k20me1`,
 `h2afz`, `h3ac`, `h3k27ac`, `h3k4me2`, `h3k4me3`, `h3k9ac`, `h3k9me3`.
+- ``keep_duplicates``: do not remove duplicates before peak calling. Defaults to `False`.
+- ``keep_multimappers``: do not remove multimappers before peak calling. Defaults to `False`.
 
 You can pass different parameters for ``macs2`` adding to :ref:`config-resources`::