Question: excessive loading time for VCF files in IGV
0
gravatar for prasundutta87
13 months ago by
prasundutta87280
prasundutta87280 wrote:

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.

igv snp visualization • 535 views
ADD COMMENTlink written 13 months ago by prasundutta87280

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

ADD REPLYlink written 13 months ago by Pierre Lindenbaum115k

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 REPLYlink modified 13 months ago • written 13 months ago by prasundutta87280

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

ADD REPLYlink written 13 months ago by genomax59k

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

ADD REPLYlink written 13 months ago by prasundutta87280

and is it fast where there is no VCF ?

ADD REPLYlink written 13 months ago by Pierre Lindenbaum115k

Yes...everything loads fine..

ADD REPLYlink written 13 months ago by prasundutta87280
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