如何解决合并snakemake中的vcf文件
运行变体调用后,我只想合并特定的输出,如d
所示。
这给了我error of missing input files
。该如何解决?
d = {"bob": ["bob:0-10.view.filtered.vcf","bob:10-20.view.filtered.vcf"]
"ann": ["ann:0-20.view.filtered.vcf","ann:20-30.view.filtered.vcf"]}
rule varcall:
input:
ref="reference.fasta",bam="bam_list"
output:
outf ="var/{chr}.view.filtered.vcf"
shell:
"""
freebayes -r {wildcards.chr} -f {input.ref} --bam-list {input.bam} -v {output.outf}
"""
wildcard_constraints:
chromosome = "|".join(chromosomes)
rule merge:
input:
lambda w: d[w.chromosome]
output:
outf = "merged/{chromosome}.vcf"
params:
lambda w: "I=" + " I=".join(d[w.chromosome])
shell:
"java -jar picard.jar GatherVcfs {params[0]} O={output.outf}"
解决方法
varcall
的输出是
outf ="var/{chr}.view.filtered.vcf"
因此字典d
应该包含目录var
:
d = {"bob": ["var/bob:0-10.view.filtered.vcf","var/bob:10-20.view.filtered.vcf"]
"ann": ["var/ann:0-20.view.filtered.vcf","var/ann:20-30.view.filtered.vcf"]}
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