Question

我想将realigner进程与indel reallignement连接起来。这是规则：

rule gatk_IndelRealigner:
    input:
        tumor="mapped_reads/merged_samples/{tumor}.sorted.dup.reca.bam",
        normal="mapped_reads/merged_samples/{normal}.sorted.dup.reca.bam",
        id="mapped_reads/merged_samples/operation/{tumor}_{normal}.realign.intervals"

    output:
        "mapped_reads/merged_sample/CoClean/{tumor}.sorted.dup.reca.cleaned.bam",
        "mapped_reads/merged_sample/CoClean/{normal}.sorted.dup.reca.cleaned.bam",
    params:
        genome=config['reference']['genome_fasta'],
        mills= config['mills'],
        ph1_indels= config['know_phy'],
    log:
        "mapped_reads/merged_samples/logs/{tumor}.indel_realign_2.log"
    threads: 8
    shell:
        "gatk -T IndelRealigner -R {params.genome}  "
        "-nt {threads} "
        "-I {input.tumor} -I {input.normal}  -known {params.ph1_indels} -known {params.mills} -nWayOut  .cleaned.bam --maxReadsInMemory 500000 --noOriginalAligmentTags --targetIntervals {input.id} >& {log}  "

这是错误：

Not all output files of rule gatk_IndelRealigner contain the same wildcards.

我想我也需要使用{tumor} _ {normal}，但我无法使用。 Snakemake：

rule all:
      input:expand("mapped_reads/merged_samples/CoClean/{sample}.sorted.dup.reca.cleaned.bam",sample=config['samples']),
           expand("mapped_reads/merged_samples/operation/{sample[1][tumor]}_{sample[1][normal]}.realign.intervals", sample=read_table(config["conditions"], ",").iterrows())

config.yml

conditions: "conditions.csv"

conditions.csv

tumor,normal
411,412

在这里你可以看到一个代码示例（用于测试目的）给出了同样的错误：

$ tree  prova/
prova/
├── condition.csv
├── config.yaml
├── output
│   ├── ABC.bam
│   ├── pippa.bam
│   ├── Pippo.bam
│   ├── TimBorn.bam
│   ├── TimNorm.bam
│   ├── TimTum.bam
│   └── XYZ.bam
└── Snakefile

这是snakemake

$ cat prova/Snakefile 
from pandas import read_table

configfile: "config.yaml"

rule all:
    input:
         expand("{pathDIR}/{sample[1][tumor]}_{sample[1][normal]}.bam", pathDIR=config["pathDIR"], sample=read_table(config["sampleFILE"], " ").iterrows()),
         expand("CoClean/{sample[1][tumor]}.bam",  sample=read_table(config["sampleFILE"], " ").iterrows()),
         expand("CoClean/{sample[1][normal]}.bam", sample=read_table(config["sampleFILE"], " ").iterrows())

rule gatk_RealignerTargetCreator:
     input:
         "{pathGRTC}/{normal}.bam",
         "{pathGRTC}/{tumor}.bam",
     output:
         "{pathGRTC}/{tumor}_{normal}.bam"
 #    wildcard_constraints:
 #        tumor = '[^_|-|\/][0-9a-zA-Z]*',
 #        normal = '[^_|-|\/][0-9a-zA-Z]*'
     run:
         call('touch ' + str(wildcard.tumor) + '_' + str(wildcard.normal) + '.bam', shell=True)



rule gatk_IndelRealigner:
    input:
        t1="output/{tumor}.bam",
        n1="output/{normal}.bam",

    output:
        "CoClean/{tumor}.sorted.dup.reca.cleaned.bam",
        "CoClean/{normal}.sorted.dup.reca.cleaned.bam",
    log:
        "mapped_reads/merged_samples/logs/{tumor}.indel_realign_2.log"
    threads: 8
    shell:
        "gatk -T IndelRealigner -R {params.genome}  "
        "-nt {threads} -I {input.t1} -I {input.n1}  & {log}  "

conditions.csv

$ more condition.csv 
tumor normal
TimTum TimBorn
XYZ ABC
Pippo pippa

感谢您的任何建议

Answer 1

我不相信你必须将两个输入文件包含在GATK IndelRealigner中。根据这个假设建立起来，你可以改变规则，使其对＃34;类型（肿瘤与正常）＆＃34;无关。文件是进程。 I read the specs here。如果我错了，请停止阅读并纠正我。

rule gatk_IndelRealigner:
    input:
        inputBAM="output/{sampleGATKIR}.bam",

    output:
        "CoClean/{sampleGATKIR}.sorted.dup.reca.cleaned.bam",
    log:
        "mapped_reads/merged_samples/logs/{sampleGATKIR}.indel_realign_2.log"
    params:
        genome="**DONT FORGET TO ADD THIS""
    threads: 8
    shell:
        "gatk -T IndelRealigner -R {params.genome}  "
        "-nt {threads} -I {input.inputBAM}   & {log}  "

通过将规则更改为bam-type agnostic（组成单词），您将获得两个优势，并且存在一个主要缺点。

优点：

现在我们只有一张外卡
我们可以独立地运行每个.bam文件的对齐方式，这对于专用的CPU应该可以让事情变得更快。

缺点：

我们现在可能会将两个基因组拷贝放到某个地方的内存中，因为这些线程现在作为单独的进程运行，不再有基因组文件的内存共享。（在我以前的位置，硬件可用性通常不是问题，因此我很擅长将所有内容分开）

我认为GATK文档设置为接受多个＆＃39; bam＆＃39;文件是因为如果您只是将其用作一次性呼叫，则需要同时列出所有文件。我们不需要，因为我们正在自动化呼叫过程。我们对1个电话或100个电话无动于衷。

snakemake管理对样本和indelrealigner

1 个答案:

优点：

缺点：