excessive loading time for VCF files in IGV

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7.0 years ago

prasundutta87 ▴ 670

Hi,

Has anyone faced an issue in which an indexed VCF file takes ages to load in IGV? If they have, is there a workaround?

I am running IGV v2.3.72 in Java 1.8 in Windows. I have tried latest version of IGV as well, it has the same issue.

snp visualization IGV • 2.5k views

ADD COMMENT • link 7.0 years ago by prasundutta87 ▴ 670

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number of samples ? number of variants ? how is it indexed : tabix+bgzip or tribble ?

ADD REPLY • link 7.0 years ago by Pierre Lindenbaum 164k

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There is only one sample..and very small number of variants (only 25) as its only for one gene..The VCF file is bgzip+tabix indexed..

ADD REPLY • link 7.0 years ago by prasundutta87 ▴ 670

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Something must be wrong. Is the genome being used correct.

ADD REPLY • link 7.0 years ago by GenoMax 147k

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It loads..but after very long time leading to time wastage..the genome used is correct only..

ADD REPLY • link 7.0 years ago by prasundutta87 ▴ 670

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and is it fast where there is no VCF ?

ADD REPLY • link 7.0 years ago by Pierre Lindenbaum 164k

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Yes...everything loads fine..

ADD REPLY • link 7.0 years ago by prasundutta87 ▴ 670

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