Kopisu is our pipeline for detecting CNVs for DNA-seq.
It can work with
Kopisu is usually used as a module inside Shiva, but can also be used stand-alone.
Tools for this pipeline
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 'namespace:namespace:key=value' -DSC,--disablescatter Disable all scatters
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.
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:
|-||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:
|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|
kopisu: use_cnmops_method: false use_freec_method: false use_xhmm_method: true amplicon_bed: <path_to_bed> xhmm: discover_params: <path_to_file> exe: <path_to_executable>
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