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biopet.biopet
Commits
2ac12ea5
Commit
2ac12ea5
authored
Jun 23, 2015
by
Sander Bollen
Browse files
Use namespace terminology (see #163)
parent
5b1fc7c4
Changes
1
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docs/pipelines/shiva.md
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2ac12ea5
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@@ -95,15 +95,15 @@ To view all possible config options please navigate to our Gitlab wiki page
<a
href=
"https://git.lumc.nl/biopet/biopet/wikis/GATK-Variantcalling-Pipeline"
target=
"_blank"
>
Config
</a>
### Required settings
|
Config Nam
e | Name | Type | Default | Function |
|
Namespac
e | Name | Type | Default | Function |
| ----------- | ---- | ---- | ------- | -------- |
| | output_dir | String | | Path to output directory |
|
-
| output_dir | String | | Path to output directory |
| Shiva | variantcallers | List[String] | | Which variant callers to use |
### Config options
|
Config Nam
e | Name | Type | Default | Function |
|
Namespac
e | Name | Type | Default | Function |
| ----------- | ---- | ----- | ------- | -------- |
| shiva | reference | String | | reference to align to |
| shiva | dbsnp | String | | vcf file of dbsnp records |
...
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@@ -136,7 +136,7 @@ The other mode, `library_variantcalling`, will call simultaneously call all libr
The config for these therefore is:
|
Config Nam
e | Name | Type | Default | Function |
|
Namespac
e | Name | Type | Default | Function |
| ----------- | ---- | ---- | ------- | -------- |
| shiva | multisample_variantcalling | Boolean | true | Default, multisample calling |
| shiva | single_sample_variantcalling | Boolean | false | Not-recommended, single sample, merged bam |
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