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Commit 38ec6a6d authored by Sascha Meiers's avatar Sascha Meiers
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small fixes

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......@@ -425,9 +425,9 @@ rule split_external_snv_calls:
vcf = lambda wc: config["snv_calls"][wc.sample]
output:
vcf = "external_snv_calls/{sample}/{chrom}.vcf"
log: "external_snv_calls/{sample}/{chrom}.vcf.log"
log: "log/{sample}/external_snv_calls.{chrom}.vcf.log"
params:
bcftools = config["bcftools"]
shell:
"({params.bcftools} view --samples {wildcards.sample} --types snps {input.vcf} {wildcards.chrom} | bcftools view --genotype het - > {output.vcf}) > {log} 2>&1"
"({params.bcftools} view --samples {wildcards.sample} --types snps {input.vcf} {wildcards.chrom} | {params.bcftools} view --genotype het - > {output.vcf}) > {log} 2>&1"
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