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Analysis tab should work on compressed vcfs and allow hg38 reference

yfarjounyfarjoun Broad InstituteDev ✭✭✭

The current analysis tab is currently almost unusable. It seems to only allow bam and vcf files, and it only has hg19 reference. The broad's main analysis pipeline is HG38, and produces compressed vcfs (.vcf.gz) and crams (.cram) on the next reference build (hg38) so all the output files are un-viewable in the in-browser IGV offered in the analysis tab.

Answers

  • KateNKateN Cambridge, MAMember, Broadie, Moderator admin

    The analysis tab is currently severely limited, due to the fact that it isn't the full IGV desktop you are used to. This "mini version", called igv.js can really only be used to preview your files. It accepts BAM, VCF, and BED file types, but CRAM is not supported. The reference is also hard-coded to the application itself, which means you only have access to hg19.

    I will put a ticket in for hg38 support, but unfortunately CRAM, and gzipped VCFs are not possible due to igv.js' own limitations. We do plan to document a way to use IGV desktop without downloading your files in the near future, as the desktop version provides all the features you are used to.

  • jasongallant1jasongallant1 East Lansing, MIMember

    Hi @KateN -- curious if there has been any progress documenting IGV Desktop method for 'download-less' file viewing? This would be pretty helpful indeed. I found some details here: http://googlegenomics.readthedocs.io/en/latest/use_cases/browse_genomic_data/igv.html, but it is kludgy at best.

  • KateNKateN Cambridge, MAMember, Broadie, Moderator admin

    There has not been any progress on that front yet, unfortunately. The workaround was not something developed by our team, so I will go find out if any documentation we didn't write exists. Otherwise, I've put in a ticket to document this ourselves.

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