Germline & Somatic short variant discovery (SNVs + Indels) for WGS & WES.
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  1. ### Variant Calling
  2. This APP developed for germline and somatic short variant discovery (SNVs + Indels).
  3. ***Supported callers***
  4. **Germline**
  5. * Haplotyper
  6. **Somatic**
  7. * TNseq (TNhaplotyper2)
  8. * TNscope
  9. * VarScan
  10. * TNhaplotyper (This caller is only available in `v0.1.0` as it is too outdated)
  11. Variant caller can be selected by setting `ture/false` in the submitted sample.csv.
  12. ***Accepted data***
  13. * TN matched WES
  14. * TN matched WGS
  15. The datatype is judged by whether the bed file is set (i.e. the `regions` in inputs).
  16. ### New Releases
  17. * The TNhaplotyper, named as TNseq in `v0.1.0`, has beed substituted by TNhaplotyper2.
  18. * The `corealigner` step has been removed.
  19. * The `vcf2maf` step has been removed. Thus, the final output is the annotated `VCF`.
  20. ### Getting Started
  21. We recommend using choppy system and Aliyun OSS service. The command will look like this:
  22. ```
  23. # Activate the choppy environment
  24. $ open-choppy-env
  25. # Install the APP
  26. $ choppy install YaqingLiu/variant-calling-latest [-f]
  27. # List the parameters
  28. $ choppy samples YaqingLiu/variant-calling-latest [--no-default]
  29. # Submit you task with the `samples.csv file` and `project name`
  30. $ choppy batch YaqingLiu/variant-calling-latest samples.csv -p Project [-l project:Label]
  31. # Query the status of all tasks in the project
  32. $ choppy query -L Label | grep "status"
  33. ```
  34. **Please note:** The `defaults` can be forcibly replaced by the settings in `samples.csv`. Therefore, there is no need to contact me over this issue.
  35. The parameters that must need contains: sample_id,normal_fastq_1,normal_fastq_2,tumor_fastq_1,tumor_fastq_2
  36. **Please carefully check**
  37. * the reference genome
  38. * bed file
  39. * the caller you want to use
  40. * whether PoN needs to be set