Output variants in VCF
seppinho opened this issue · 10 comments
Is this a feature you're currently working on now?
yes exactly!
Any updates on this feature? I've made a basic script for another tool, MitoSeek, that takes their output file into a VCF. I might try to adapt that script for this application!
hi, sorry worked on the homoplasmic part and didn't have the chance to finish this. is your script available?
best.
Sebastian
I have a working python script
can you share it?
I'd be happy to, do you want me to fork your repo and add it there? Or can I push it to this branch?
Hey, I wrote a python script to convert the variants result to VCF format. However its hard to deal with deletion, because it's show as 'D' in the result, and VCF show deletion like:
For simple insertions and deletions in which either the REF or one of the ALT alleles would otherwise be null/empty, the REF and ALT Strings must include the base before the event (which must be reflected in the POS field), unless the event occurs at position 1 on the contig in which case it must include the base after the event
If you can change the result of indel like this and also pos - 1, it would be far more easy to convert.
My current solution is read the reference rCRS to get the REF and ALT when it's deletion.
Now integrated
Sorry for this reply outside the original topic, but I'm interested in the reply of @jpt1016:
Any updates on this feature? I've made a basic script for another tool, MitoSeek, that takes their output file into a VCF. I might try to adapt that script for this application!
@jpt1016, do you have that basic script publicly available? I couldn't find neither this script anywhere nor a way to contact you directly about this.