igvtools index memory consumption

[Vered Sokolovsky]

Hi,

I am using igvtools (cli) v2.3.81  in order to index a 7Gb size vcf file. It seems that I must run igvtools with java settings of -Xmx8g for this to complete successfully - less than that causes out-of-memory error.

I tried running the same command (igvtools index) on the same vcf file with a very old version of igvtools I have (v1.5.15), and it completed successfully with java settings of only -Xmx1500m

So I wonder if this means that igvtools needs memory at least the size of the file it is indexing ? and if so, could this be fixed ?

Another thing that I've noticed is that the idx files created by the two versions are similar in size, but have different checksum. Is the result compatible between the 2 versions?

thank you,

Vered     

[James Robinson]

I will look into this.   There is no direct correlation between file size and memory requirement that I am aware of.    Indexes created with 1.5 should be compatible with the current IGV,  but the reverse is not true.   However, for files of this size I recommend you use tabix,  it is the de-facto standard for vcf files and will compress as well as index the file.  Do a websearch for "samtools tabix" if you are not familiar with it.

It would be helpful if you could open a git issue since I won't be able to look at this right away.

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