Problem with Delly-Sansa

[Aleksia Vaattovaara]

Hi,

I have tried to annotate the result vcf file from Delly with Sansa with following command

sansa annotate -g genes.gtf.gz delly.vcf

And I get following report:

[2020-Dec-16 14:52:51]  sansa annotate -g genes.gtf.gz delly.vcf
[2020-Dec-16 14:52:53] Parse SV annotation database
[2020-Dec-16 14:52:53] Parsed 6552 out of 6552 VCF/BCF records.
[2020-Dec-16 14:52:56] BED feature parsing
terminate called after throwing an instance of 'boost::wrapexcept<boost::bad_lexical_cast>'
  what():  bad lexical cast: source type value could not be interpreted as target
Aborted

So I assume the issue is with gtf file (I also tried with gff3 file and that produced the same error).

Any idea how to solve this problem? I would be very thankful of any help.

Best,

Aleksia

[Tobias Rausch]

Hi Aleksia,

The Ensembl GFF3 files usually start with ##gff and that's what I currently use to distinguish the formats. I agree that's not ideal. I just committed code that now checks the file endings. 'gff.gz' and 'gff3.gz' as well as 'gtf.gz' are now properly assigned. Can you please try again with the latest code?

Thanks, Tobias

[Aleksia Vaattovaara]

Hi Tobias,

Thank you so much for a quick reply. I re-installed the program through bioconda. Unfortunately I still got the same error message (for both gtf and gff3). But when I added ##gff in the beginning of gff3 file it worked. So the problem was solved that way.

Thank you!

Best wishes,

Aleksia

[Tobias Rausch]

Bioconda only updates with a new release. Only the Github code is up-to-date but if ##gff solved it then that's fine I guess.

Best, Tobias