IGV 3.0 snapshots very slow compared to IGV 2.3

[Michael Heskett]

Hi team,

I enjoy the new features of IGV 3 but the same batch script I use to make snapshots of somatic variants takes about 50 times longer than IGV2.3. Is there a setting I can use on load to make loading each variant locus quicker? 

Best,

Michael

[James Robinson]

There is no "load quick" setting.    We weren't aware of this, can you post a script that reproduces the problem?  If possible open a git issue with the script included at github.com/igvteam/igv/issues.

Jim

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[Michael Heskett]

The script looks just like your example script. With igv 2.3 it takes a few seconds for each variant, with igv 3.0 it takes minutes per variant. 

new

genome hg19

load  /mynormal.bam

load  /mytumor.bam

snapshotDirectory  /snaphots/

goto chr1:70503880-70503980

sort position

collapse

snapshot

goto chr1:114400333-114400433

sort position

collapse

snapshot

goto chr1:150482359-150482459

sort position

collapse

snapshot

goto chr1:176054897-176054997

sort position

collapse

snapshot

... repeat many times

$ /opt/installed/jdk1.8.0_111/bin/java -Xmx12g -jar /heskett/tools/IGV_3.0_beta/igv.jar --batch=bactchscript.igvsnapshot.txt

Running on 64 bit CentOS

[James Robinson]

Thanks, the script is helpful.   "Variant" doesn't help me much,  could be a vcf file, a bed file,  any number of other file types.   I will do some profiling and see what's going on.

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