2 changed files with 3 additions and 3 deletions
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README.md
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| This APP developed for somatic short variant discovery (SNVs + Indels). | This APP developed for somatic short variant discovery (SNVs + Indels). | ||||
| ***Supported callers*** | ***Supported callers*** | ||||
| * TNhaplotyper2 | |||||
| * TNseq (TNhaplotyper2) | |||||
| * TNscope | * TNscope | ||||
| * VarScan | * VarScan | ||||
| * TNhaplotyper (This caller is only available in `v0.1.0` as it is too outdated) | * TNhaplotyper (This caller is only available in `v0.1.0` as it is too outdated) | ||||
| The datatype is judged by whether the bed file is set (i.e. the `regions` in inputs). | The datatype is judged by whether the bed file is set (i.e. the `regions` in inputs). | ||||
| ### New Releases | ### New Releases | ||||
| * The TNhaplotyper, also named as TNseq in `v0.1.0`, has beed substituted by TNhaplotyper2. | |||||
| * The TNhaplotyper, named as TNseq in `v0.1.0`, has beed substituted by TNhaplotyper2. | |||||
| * The `corealigner` step has been removed. | * The `corealigner` step has been removed. | ||||
| * The `vcf2maf` step has been removed. Thus, the final output is the annotated `VCF`. | * The `vcf2maf` step has been removed. Thus, the final output is the annotated `VCF`. | ||||
tasks/TNhaplotyper2.wdl → tasks/TNseq.wdl
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| task TNhaplotyper2 { | |||||
| task TNseq { | |||||
| File ref_dir | File ref_dir | ||||
| File dbsnp_dir | File dbsnp_dir | ||||
| String sample | String sample |
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