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support for GATK/IGV vcf.idx files #1019

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thon-deboer opened this Issue Mar 8, 2018 · 3 comments

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@thon-deboer

thon-deboer commented Mar 8, 2018

I have a customer that also uses IGV and they have configured their pipeline to produce the vcf.idx files for VCF files in stead of using bgzip/tabix indices which JBROWSE prefers.

Does JBROWSE support IDX indices? If not, what would it take to do so?

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rbuels commented Mar 8, 2018

We don't support that right now but it would be nice to have for compatibility with IGV. Are these .idx files being made by GATK? Do you by chance have any place where we can get sample data to use in development on this?

@rbuels rbuels changed the title from Does JBROWSE support the igvtools IDX index for VCF files? to support for GATK/IGV vcf.idx files Mar 8, 2018

@rbuels rbuels added the help wanted label Mar 8, 2018

@thon-deboer

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thon-deboer commented Mar 8, 2018

Sure...But it is just created by IGV's igvtools I believe...

1801160099-N32519_26611_S51_56704.hard-filtered.zip

@rbuels rbuels added this to the 1.14.0 milestone Mar 28, 2018

@rbuels rbuels modified the milestones: 1.14.0, 1.14.1 Apr 10, 2018

@rbuels rbuels self-assigned this May 1, 2018

@rbuels rbuels added the in progress label May 1, 2018

@rbuels rbuels closed this in 69cb48e May 1, 2018

@rbuels rbuels removed the in progress label May 1, 2018

@thon-deboer

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thon-deboer commented May 1, 2018

WOOT!

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