Hello, I am using the pipeline to benchmark small variant amongst deepvariant VCFs. These VCFs are generated with same reference genome. I wonder what filter_contigs do and could I skip this. It seems this step only supported for pre-defined genome.

Hello Hanh, If you dont want additional contigs to be skipped and only wanna take main chromosomes (chr1-22 X and Y) into account, you can use filter_contigs. And yes, unfortunately, that is right, it only works for human genome. I didnt take other genomes properly back then. What type of genome you have?

Thank you for your reply. I am working with non-model genomes. I am thinking that I will skip filter_contigs, as I am want to compare on whole genome.

Yes, I think using filter_contigs may crush your run. Please let me know if you have any issues.