Reference-Based assembly with reference as an output

[Phismil]

Good day Deren and Isac, Thank you for maintaining and updating the repository. In reference-based assembly, is there any way to print the matching loci within reference sequence itself as one of the samples in the output sequence files? I usually use third party packages to convert .vcf/.bam to a consensus sequence after phasing etc. I am wondering there might be a more straightforward solution for this task during loci assemblies by Ipyrad itself? Thank you in advance

[isaacovercast]

Hello! In fact there is a quite straightforward way to include the reference sequence in the output files. There is a hackersonly parameter which you can set by running the analysis inside a jupyter notebook, like this:

import ipyrad
data = ipyrad.load_json("/tmp/ipyrad-test/peddradnames.json")
data.hackersonly.exclude_reference = True
data.run(steps="7", auto=True)

If you want to run CLI you can edit the json file by hand and set this parameter to True, but hand editing the json file is not recommended generally. Give that a shot and let me know how it goes.

Good luck!