Hi, When running the nf-core/rardisease full_test I get an output, for instance in the "call_snvs" folder, that only covers regions in chr21. I see that the "target_bed" parameter references a file that only specifies regions on chr21. I would like to scale up the analysis a bit, without putting unnecessary strain on the server, like call variants in the whole genome and then annotate exon and ClinVar-variants (plus some padding). Could I achive that by setting parameters as of now? If not is it possible/sensible to run the pipeline without using the "target_bed" parameter if there is enough computing power? In the end I would like to try to run some validation with Genome In Bottle Samples.

Hello, Halfdan! Yes, if you have enough computing power you can run the pipeline without target_bed parameter. But the reference file in the full_test also points to a subset of the genome, which is why you are probably seeing variants from only chr21. From what I can tell, variants are called from whole genome by default for WGS samples. Variants are restricted to regions in target_bed only for WES samples.

Ah, okey, thankyou . I could have checked the sized of the fastqs and figured out. I will try with whole genome input then and see what the results look like then.

Great! Let me know how it goes

Hi again Ram. I am now running with whole genome input but the output, like the vcf.gz file in annotate_snv/genome, still seems to be limited to chr21. Could it be so that the target_wgs.interval_list, or some other config file is limiting the analysis to chr 21?

I see now the re are a lot of reference files covering only chr21. I will do my best to repalce them with whole genome versions.

Does this include annotation steps as well @halfdan?

I feel fairly confident it does @Ram. I used a config file modified from test_full and prepared reference files following https://github.com/fa2k/raredisease-configs, thank you @Marius Bjørnstad. The GIAB Ashkenazi trio seems to have run as well, soon finished.