Commit 03852d0d authored by Peter van 't Hof's avatar Peter van 't Hof

Merge branch 'fix-biopet-472' into 'develop'

docs on xhmm

See merge request !491
parents 2705817e 9ae30190
# Kopisu
## Introduction
Kopisu is our pipeline for detecting CNVs for DNA-seq.
It can work with `bam` files.
Kopisu is usually used as a module inside Shiva, but can also be used stand-alone.
## Tools for this pipeline
* [FreeC](
* [cn.mops](
* [XHMM](
## Usage
biopet pipeline kopisu --help
Arguments for Kopisu:
-BAM,--inputbamsarg <inputbamsarg> Bam files (should be deduped bams)
-config,--config_file <config_file> JSON / YAML config file(s)
-cv,--config_value <config_value> Config values, value should be formatted like 'key=value' or
-DSC,--disablescatter Disable all scatters
## Methods
For CNV calling, Kopisu supports three methods, each with different use cases:
* FreeC: Use for WGS or Exomes. For WGS, a control sample set is not required
* Cn.mops: Use for Exomes. Must be used on a set of samples, preferably with N>20. Do not use on low-coverage samples.
* XHMM: Use for Exomes or targeted approach. Number of target regions _must_ be larger than the amount of samples. Use with N >= 40.
All three methods can be run concurrently. However, we do not yet provide any merging of calls, since output formats vary widely.
### Freec
### Cn.mops
### XHMM
When using the XHMM method, one _must_ provide a target bed file.
XHMM cannot work without it.
Additionally, the XHMM method requires the path to a parameters file for XHMM.
Please see the XHMM website for what this file should contain.
This means the following config values are required:
| Namespace | Name | Type | Default | Meaning |
| --------- | ---- | ---- | ------- | ------- |
| - | amplicon_bed | Path | - | Path to target bed file |
| xhmm | discover_params | Path | - | Path to XHMM params file |
It is recommended you use at least 40 samples with this method.
One should also have more _covered_ target regions than there are samples.
This means this method is not suited for very small target kits.
Please note that it is _not_ possible to run this method without GATK dependencies.
Additional optional config values:
| Namespace | Name | Type | Default | Meaning |
| --------- | ---- | ---- | ------- | ------- |
| xhmm_normalize | normalize_method | String | PVE_mean | The normalization method to use |
| xhmm_normalize | pve_mean_factor | Float | 0.7 | Factor for PVE mean normalization |
**XHMM example**
use_cnmops_method: false
use_freec_method: false
use_xhmm_method: true
amplicon_bed: <path_to_bed>
discover_params: <path_to_file>
exe: <path_to_executable>
## Getting Help
If you have any questions on running Kopisu, suggestions on how to improve the overall flow, or requests for your favorite CNV related program to be added, feel free to post an issue to our issue tracker at [GitHub](
Or contact us directly via: [SASC email](
\ No newline at end of file
......@@ -152,7 +152,7 @@ Shiva furthermore supports three modes. The default and recommended option is `m
During this mode, all bam files will be simultaneously called in one big VCF file. It will work with any number of samples.
On top of that, Shiva provides two separate modes that only work with a single sample.
Those are not recommend, but may be useful to those who need to validate replicates.
Those are not recommended, but may be useful to those who need to validate replicates.
Mode `single_sample_variantcalling` calls a single sample as a merged bam file.
I.e., it will merge all libraries in one bam file, then calls on that.
......@@ -167,7 +167,16 @@ The config for these therefore is:
| shiva | single_sample_variantcalling | Boolean | false | Not-recommended, single sample, merged bam |
| shiva | library_variantcalling | Boolean | false | Not-recommended, single sample, per library |
## CNV calling
In addition to standard variant calling, Shiva also supports CNV calling.
One can enable this option by setting the `cnv_calling` config option to `true`.
For CNV calling Shiva uses the [Kopisu]( as a module.
Please see the documentation for Kopisu.
## Example configs
**Config example**
``` yaml
......@@ -189,6 +198,21 @@ variantcallers:
- haplotypecaller_gvcf
**Additional XHMM CNV calling example**
cnv_calling: true
use_cnmops_method: false
use_freec_method: false
use_xhmm_method: true
amplicon_bed: <path_to_bed>
discover_params: <path_to_file>
exe: <path_to_executable>
## References
* Shiva follows the best practices of GATK: [GATK best practices](
......@@ -14,6 +14,7 @@ pages:
- Flexiprep (QC): 'pipelines/'
- Gears (Metagenome): 'pipelines/'
- Gentrap (RNA-seq): 'pipelines/'
- Kopisu (CNV Calling): 'pipelines/'
- Mapping (Alignment): 'pipelines/'
- Sage: 'pipelines/'
- Shiva (variantcalling): 'pipelines/'
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