Dear all,
I have files like this:
bob/dad.vcf
bob/mom.vcf
bob/son.vcf
john/dad.vcf
john/mom.vcf
john/son.vcf
steve/dad.vcf
steve/mom.vcf
steve/son.vcf
I want to find the intersect and see how many dads, moms and sons are in common, i.e. bob/dad.vcf with john/dad.vcf, then bob/dad.vcf with steve/dad.vcf and so on. The problem is I do not know how to put directories as wildcards as well since they are different:
(DIR, SAMPLES) =glob_wildcards('/path/to/{dir}/{sample}.vcf')
rule all:
input:
expand("{sample}.common_bob_john", zip, sample=SAMPLES, dir=DIR)
rule bedtools_common:
input:
in1="/path/to/bob/{sample}.vcf",
in2 = "/path/to/john/{sample}.vcf"
output:
out1="{sample}.common_bob_john"
shell:
"""
/Tools/bcftools-1.10.2/bcftools isec {input.in1} {input.in2} -p {output.out1}
"""