Genome Size and VCF2RADdata

[andrea-bellucci]

Hello. I was starting to play around and trying to import my vcf file. I get this error

Indexing VCF.
[E::hts_idx_check_range] Region 536950282..536950283 cannot be stored in a tbi index. Try using a csi index
Error in value[3L] : index build failed

I am assuming it is because chromosome size is too big for tabix. Checking VCF2RADdata it can be seen that calls Rsamtools::TabixFile for vcf indexing which i assume it calls tabix eventually. But there s no option in Rsamtools::TabixFile to change index tipe and having a csi index in the same folder would help because VCF2RADdata check for .tbi index presence.
So i am a bit stuck here. Any idea how to get around this without splitting all chromosomes in the reference?
Thanks

[lvclark]

This is something I can definitely fix in the code. I know that VariantAnnotation can read csi indices, at least.

…

On Mon, Feb 20, 2023, 9:31 AM andrea-bellucci ***@***.***> wrote: Hello. I was starting to play around and trying to import my vcf file. I get this error Indexing VCF. [E::hts_idx_check_range] Region 536950282..536950283 cannot be stored in a tbi index. Try using a csi index Error in value[3L] <http://cond> : index build failed I am assuming it is because chromosome size is too big for tabix. Checking VCF2RADdata it can be seen that calls Rsamtools::TabixFile for vcf indexing which i assume it calls tabix eventually. But there s no option in Rsamtools::TabixFile to change index tipe and having a csi index in the same folder would help because VCF2RADdata check for .tbi index presence. So i am a bit stuck here. Any idea how to get around this without splitting all chromosomes in the reference? Thanks — Reply to this email directly, view it on GitHub <#35>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADG72KBZRMGBZHZI7DYFWRLWYN52TANCNFSM6AAAAAAVB6LR5Y> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[lvclark]

Ok, I just pushed a fix to GitHub, and it should propagate to R-universe within a few hours. If you bgzip and csi-index your VCF before running VCF2RADdata, it should work. Let me know if you run into issues.

[andrea-bellucci]

Thanks a lot for the help. I will try it out asap.

[andrea-bellucci]

Works great now providing vcf.bgz file and csi index. Thanks again for the help!