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. * All callers are <u>**not activated by default**</u>, which means the default setting is `false`.
  5. * You need to manually set the caller to `true` in the submitted sample.csv.
  6. * The fields corresponding to these callers include `haplotyper`, `tnseq`, `tnscope`, `varscan`.
  7. ***Germline***
  8. * Haplotyper
  9. ***Somatic***
  10. * TNseq (TNhaplotyper2)
  11. * TNscope
  12. * VarScan
  13. * TNhaplotyper (This caller is only available in `v0.1.0` as it is too outdated)
  14. **Accepted Data**
  15. * TN matched WES for somatic variant calling
  16. * TN matched WGS for somatic variant calling
  17. * Normal-only WES for germline variant calling
  18. * Normal-only WGS for germline variant calling
  19. The datatype is judged by whether the bed file is set (i.e. the `regions` in inputs).
  20. ### New Releases
  21. * The TNhaplotyper, named as TNseq in `v0.1.0`, has beed substituted by TNhaplotyper2.
  22. * The `corealigner` step has been removed.
  23. * The `vcf2maf` step has been removed. Thus, the final output is the annotated `VCF`.
  24. ### Getting Started
  25. We recommend using choppy system and Aliyun OSS service. The command will look like this:
  26. ```
  27. # Activate the choppy environment
  28. $ open-choppy-env
  29. # Install the APP
  30. $ choppy install YaqingLiu/variant-calling-latest [-f]
  31. # List the parameters
  32. $ choppy samples YaqingLiu/variant-calling-latest [--no-default]
  33. # Submit you task with the `samples.csv file` and `project name`
  34. $ choppy batch YaqingLiu/variant-calling-latest samples.csv -p Project [-l project:Label]
  35. # Query the status of all tasks in the project
  36. $ choppy query -L Label | grep "status"
  37. ```
  38. **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.
  39. The parameters that must need contains: sample_id,normal_fastq_1,normal_fastq_2,tumor_fastq_1,tumor_fastq_2
  40. **Please carefully check**
  41. * the reference genome
  42. * bed file
  43. * the caller you want to use
  44. * whether PoN needs to be set