Hi everyone, I need your help resolving this problem.
I'm working on diploide chromosome, and each chromosome has 2 haplotypes.
To run my snakemake, i started with two repertoire containing:
- Haplotype: * chr_1.gff * chr_2.gff
i need to run Bedtools to intersect Chr_1.gff in Haplotype with Chr_1.gff in NLR-annotator. The problem is that generate two output, chr_1 [haplotype] vs chr_1[NLR-Annotator] and chr1_[haplotype] vs chr_2 [NLR-Annotatr]. i need only the intersection when the filenames match together.
I used wildcards but it doesn't work.
Thank you in advance