Commit 259dd8e7 authored by Peter van 't Hof's avatar Peter van 't Hof
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Merge branch 'feature-shiva-docs' into 'develop'

add amplicon bed file documentation

Added documentation about amplicon_bed and regions_of_interest bed files.

closes #297 

See merge request !356
parents ea9993b3 535570c3
......@@ -135,6 +135,17 @@ To view all possible config options please navigate to our Gitlab wiki page
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.
### Exome variant calling
If one calls variants with Shiva on exome samples and a ```amplicon_bed``` file is available, the user is able to add this file to the config file.
When the file is given, the coverage over the positions in the bed file will be calculated plus the number of variants on each position. If there is an interest
in a specific region of the genome/exome one is capable to give multiple ```regionOfInterest.bed``` files with the option ```regions_of_interest``` (in list/array format).
A short recap: the option ```amplicon_bed``` can only be given one time and should be composed of the amplicon kit used to obtain the exome data.
The option ```regions_of_interest``` can contain multiple bed files in ```list``` format and can contain any region a user wants. If multiple regions are given,
the pipeline will make an coverage plot over each bed file separately.
### Modes
Shiva furthermore supports three modes. The default and recommended option is `multisample_variantcalling`.
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