Question: excessive loading time for VCF files in IGV
0
gravatar for prasundutta87
7 months ago by
prasundutta87170
prasundutta87170 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 • 381 views
ADD COMMENTlink written 7 months ago by prasundutta87170

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

ADD REPLYlink written 7 months ago by Pierre Lindenbaum108k

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 7 months ago • written 7 months ago by prasundutta87170

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

ADD REPLYlink written 7 months ago by genomax50k

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

ADD REPLYlink written 7 months ago by prasundutta87170

and is it fast where there is no VCF ?

ADD REPLYlink written 7 months ago by Pierre Lindenbaum108k

Yes...everything loads fine..

ADD REPLYlink written 7 months ago by prasundutta87170
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