diff --git a/docs/pipelines/shiva.md b/docs/pipelines/shiva.md index c8ca27b285e521118f3900b577d8391ff9e98d9f..25783b8793306f50a7f5a604e4bf6c82ec6afb7c 100644 --- a/docs/pipelines/shiva.md +++ b/docs/pipelines/shiva.md @@ -118,6 +118,9 @@ To view all possible config options please navigate to our Gitlab wiki page | vcffilter | min_samples_pass | Integer | 1 | Minimum amount of samples which pass custom filter (requires additional flags) | | vcffilter | filter_ref_calls | Boolean | true | Remove reference calls | +Since Shiva uses the [Mapping](../mapping.md) pipeline internally, mapping config values can be specified as well. +For all the options, please see the corresponding documentation for the mapping pipeline. + ### Modes Shiva furthermore supports three modes. The default and recommended option is `multisample_variantcalling`.