FORMAT 'CN' is not defined in the header

[zihhuafang]

Hi David,

Thanks for developing SVIM.
I am filtering SV called by SVIM and ran into this issue with the variants.vcf.
There are DUP_TAN variants with GT:CN:DP:AD, but CN was not defined in the header.
I checked wiki and did not find any information about CN.
I am not sure what to do with these variants since these are pass variants.

Would love to get your insights about it.
Thanks!
Best wishes,
Zih-Hua

[eldariont]

Hi Zih-Hua,

thanks for your question and for spotting this issue. I recently added the CN tag in response to a user's request (see #24) and obviously forgot to define it in the header. This should be fixed now with the most recent commit.

The CN tag stores the copy number of a tandem duplication. For instance, a copy number of 3 would mean that the region between POS and END was duplicated two times so that there are now 3 tandem copies.

Let me know if you have further questions.
Cheers
David

[zihhuafang]

Hi David,

Thanks for the reply.
I use svim=1.3.0=py_0 (installed via bioconda) and encountered this issue.
According to the Changelog, it should be fixed.
Should I use git instead to have the most recent commit?

Cheers,
Zih-Hua

[eldariont]

Hi Zih-Hua,

yes, I updated only the github repository while conda is still on the previous version (1.3.0). I update conda regularly but not after every change because most changes, including this one, are not huge.

With the last commit I only added one line to the header that defines the CN tag. If you want to install this latest version you need to install svim from the github repo with

git clone https://github.com/eldariont/svim.git
cd svim
pip install .

Best
David