Hello,

I want to do variant calling of my multiple bam files.

rule bcftools:
    input:
        ref="genome.fa",
        bam="/path/to/bam_list",
    output:
        outf ="chr.vcf"
    shell:
        "bcftools mpileup -f {input.ref} --bam-list {input.bam} |"  
        "bcftools call -vcO v {output.outf}"

bam_list:

bob.bam
john.bam
carl.bam
...
so on

If I do not specify the path of each bam file in the bam_list, it cannot find it. But if I specify in my final vcf file, the path will be included in each column of the genotype name (which is annoying and long since I have many bam files). How can I specify one single path to all my bam files?

EDIT: I specified the working directory and it works, if there are any other solutions good to know anyway.