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fix documentation bug
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Smith Nicholas committed Jul 6, 2022
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4 changes: 2 additions & 2 deletions docs/source/prepare.rst
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Expand Up @@ -157,7 +157,7 @@ RNA Variant Calling dictionary
Variant Calling originating from RNA-seq data may be useful for researchers who do not have access to variant calls from genomic data. While variant calling from WES and WGS technologies may be more traditional (and reliable), we have found that variant calling from RNA-Seq data can provide additional evidence for the underlying causes of aberrant expression or splicing.
The RNA variant calling process uses information from multiple samples (as designated by the ``groups`` variable) to improve the variant calling process. However, the larger the group size, the more costly the computation is in terms of time and resources. When building the sample annotation table, take this into account. For the most accurate variant calls include many samples in each ``DROP_GROUP`` group, but in order to speed up computation, separate samples into many groups.

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Parameter Type Description Default/Examples
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groups list groups that should be executed in this module. If not specified or ``null`` all groups are used. ``- group1``
Expand All @@ -174,7 +174,7 @@ repeat_mask character Location of the RepeatMask ``.bed`` file. Refe
minAlt numeric Integer describing the minimum required reads that support the alternative allele. We recommend a minimum of 3 if further filtering on your own. 10 otherwise. ``3``
hcArgs character String describing additional arguments for GATK haplocaller. For expert tuning. ``""``

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Modularization of DROP
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