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Snakefile
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Snakefile
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configfile: "config.yml"
rule xpclr:
input:
vcf='data/ag1000g.crosses.phase1.ar3sites.3L.vcf.gz',
tbi='data/ag1000g.crosses.phase1.ar3sites.3L.vcf.gz.tbi',
samplesA='samplesA.txt',
samplesB='samplesB.txt'
output:
txt='output/results.txt'
params:
logging=10,
stop=1000000
shell:
"xpclr --format vcf "
"--input {input.vcf} "
"--out {output.txt} "
"--samplesA {input.samplesA} "
"--samplesB {input.samplesB} "
"--stop {params.stop} "
"--chr 3L "
"-V {params.logging}"
rule down_vcf:
output:
vcf='data/ag1000g.crosses.phase1.ar3sites.3L.vcf.gz',
params:
path=config["path"]
shell:
"curl -L {params.path} > {output.vcf}"
rule index_vcf:
input:
vcf="{path}.vcf.gz"
output:
tbi="{path}.vcf.gz.tbi"
shell:
"tabix -p vcf {input.vcf}"