Question: excessive loading time for VCF files in IGV
0
gravatar for prasundutta87
10 months ago by
prasundutta87190
prasundutta87190 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 • 469 views
ADD COMMENTlink written 10 months ago by prasundutta87190

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

ADD REPLYlink written 10 months ago by Pierre Lindenbaum112k

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 10 months ago • written 10 months ago by prasundutta87190

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

ADD REPLYlink written 10 months ago by genomax55k

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

ADD REPLYlink written 10 months ago by prasundutta87190

and is it fast where there is no VCF ?

ADD REPLYlink written 10 months ago by Pierre Lindenbaum112k

Yes...everything loads fine..

ADD REPLYlink written 10 months ago by prasundutta87190
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