使用snakemake合并多个vcf文件

Question

我正在尝试使用snakemake按染色体合并几个vcf文件。我的文件是这样的，正如你所看到的，有不同的坐标。合并所有chr1A和所有chr1B的最佳方法是什么？

chr1A:0-2096.filtered.vcf
chr1A:2096-7896.filtered.vcf
chr1B:0-3456.filtered.vcf
chr1B:3456-8796.filtered.vcf

我的伪代码：

chromosomes=["chr1A","chr1B"]

rule all:
    input: 
        expand("{sample}.vcf", sample=chromosomes)

rule merge:
    input:
        I1="path/to/file/{sample}.xxx.filtered.vcf",
        I2="path/to/file/{sample}.xxx.filtered.vcf",
    output:
        outf ="{sample}.vcf"
    shell:
        """
        java -jar picard.jar GatherVcfs I={input.I1} I={input.I2} O={output.outf}
        """

编辑：

workdir: "/media/prova/Maxtor2/vcf2/merged/"

import subprocess

d = {"chr1A": ["chr1A:0-2096.flanking.view.filtered.vcf", "chr1A:2096-7896.flanking.view.filtered.vcf"],
     "chr1B": ["chr1B:0-3456.flanking.view.filtered.vcf", "chr1B:3456-8796.flanking.view.filtered.vcf"]}


rule all:
    input:
        expand("{sample}.vcf", sample=d)

def f(w):
    return d.get(w.chromosome, "")


rule merge:
    input:
        f
    output:
        outf ="{chromosome}.vcf"
    params:
        lambda w: "I=" + " I=".join(d[w.chromosome])
    shell:
        "java -jar /home/Documents/Tools/picard.jar GatherVcfs {params[0]} O={output.outf}"

Answer 1

我能重现你的窃听器。当约束通配符时，它起作用：

d = {"chr1A": ["chr1A:0-2096.flanking.view.filtered.vcf", "chr1A:2096-7896.flanking.view.filtered.vcf"],
     "chr1B": ["chr1B:0-3456.flanking.view.filtered.vcf", "chr1B:3456-8796.flanking.view.filtered.vcf"]}

chromosomes = list(d)

rule all:
    input:
        expand("{sample}.vcf", sample=chromosomes)

# these tell Snakemake exactly what values the wildcards may take
# we use "|" to create the regex chr1A|chr1B
wildcard_constraints:
    chromosome = "|".join(chromosomes)

rule merge:
    input:
        # a lambda is an unnamed function
        # the first argument is the wildcards
        # we merely use it to look up the appropriate files in the dict d
        lambda w: d[w.chromosome]
    output:
        outf = "{chromosome}.vcf"
    params:
        # here we create the string 
        # "I=chr1A:0-2096.flanking.view.filtered.vcf I=chr1A:2096-7896.flanking.view.filtered.vcf"
        # for use in our command
        lambda w: "I=" + " I=".join(d[w.chromosome])
    shell:
        "java -jar /home/Documents/Tools/picard.jar GatherVcfs {params[0]} O={output.outf}"

它也应该在没有约束的情况下工作；这看起来像是Snakemake中的一个bug。