Open jcw349 opened 3 days ago
Sorry about that @jcw349! When writing VCF, "NC_045512" is hardcoded! We should be able to do better than that.
Hopefully something like this will work for you in the meantime?:
sed -e 's/^NC_045512/NC_009942/;' usher/mutations.vcf > usher/mutations.renamed.vcf
Sorry about that @jcw349! When writing VCF, "NC_045512" is hardcoded! We should be able to do better than that.
Hopefully something like this will work for you in the meantime?:
sed -e 's/^NC_045512/NC_009942/;' usher/mutations.vcf > usher/mutations.renamed.vcf
No worries!! Thank you for looking into this and sharing a solution to fix the VCF.
The matUtil extract -i <json_file> -o <mat.pb>
also seems to be labeling non-covid trees the same reference, NC_045512. It was in the output MAT file too. Not sure if that'll have a big impact on doing other things with the file?
For now I remade the MAT.pb using UShER, which did end up using NC_009942, but it didn't keep all of the same things I had initially put into the nextstrain tree like filters and colors, etc.
Yes, the MAT protobuf contains only the mutation annotated tree, not the other many things that can be layered onto Nextstrain's Auspice JSON format. The matUtils extract options for adding in a reference, metadata etc. are only used when generating JSON output AFAIK.
Sorry, what I mean is, when I tried to use matUtil extract
to convert the Auspice json to MAT protobuf, for some reason the MAT.pb ended up having the NC_045512 in it too, even though that's not in the input json.
Yes, NC_045512 is hardcoded when importing JSON, sorry. Does auspice/WNV-global.json contain "NC_009942" anywhere in it? (If you're able to share auspice/WNV-global.json privately then I can take a look at how matUtils might figure out what the reference name should be.)
Hi,
I am trying to convert a West Nile virus auspice tree to a MAT. The
matUtils extract
keeps including "NC_045512" in the output file, but it's not in my input auspice file.matUtils extract -i auspice/WNV-global.json -o usher/WNV-global.pb
I tried specifying the reference files and metadata as well, but it's still creating the same MAT.
matUtils extract -i auspice/WNV-global.json -g config/reference.gtf -f config/reference.fasta -o usher/WNV-global.pb
reference: NC_009942
VCF from the output MAT:
matUtils extract -i usher/WNV-global.pb -g config/reference.gtf -f config/reference.fasta -v usher/mutations.vcf
First 5 rows and 12 columns of the vcf:
Not sure what I'm doing wrong.
Thank you, Jade W