Snakemake: unknown output/input files after splitting by chromosome
问题 To speed up a certain snakemake step I would like to: split my bamfile per chromosome using bamtools split -in sample.bam --reference this results in files named as sample.REF_{chromosome}.bam perform variant calling on each resulting in e.g. sample.REF_{chromosome}.vcf recombine the obtained vcf files using vcf-concat (VCFtools) using vcf-concat file1.vcf file2.vcf file3.vcf > sample.vcf The problem is that I don't know a priori which chromosomes may be in my bam file. So I cannot specify