Uploading VCF track onto JBrowse 1.16.8

Question

[rajeshpn]

Hi I could upload fasta file using "Open Sequence file" and gff3, BAM files through "Open track file or URL" from top menu bar on JBrowse version 1.16.8. But when I tried to upload vcf file, JBrowse is recognizing but not uploading.

Did any of you face the same issue? Is this capability version dependent? If so, what version?

Thanks for your help in advance

Rajesh

Answer 1

[cmdcolin]

JBrowse v1 does not have a plaintext VCF adapter. You must create a "tabix indexed VCF" and then add both the file.vcf.gz and file.vcf.gz.tbi

You can create a tabix index using

   bgzip my.vcf
   tabix -p vcf my.vcf.gz

note: jbrowse 2 does have a plaintext vcf adapter

[rajeshpn]

Thank you. I'll try your suggestions. Appreciate your response.

Yes. With JBrowse2, it is straightforward.

With previous version of JBrowse, I can select BAM and index files of multiple samples of the same species together. But in JBrowse 2, I need to do it one by one I believe.

[cmdcolin]

thanks for noting this. indeed, the multi-track drag and drop panel is not in jbrowse 2 yet. if you think its a valuable feature we could definitely consider it

[rajeshpn]

Since the users got used to multi-drag option, taking that away becomes. I think it is a useful feature as it saves a lot of time especially when the users deal with multiple datasets,