Parse VCF files

[dianalemos]

I don't know if here is the right place to ask this, probably not. If someone knows where is the right place please tell me. I'm using VCFFileReader to read the file and then CloseableIterator<VariantContext> vc = fileReader.iterator(); while(vc.hasNext()){ VariantContext v = vc.next();

to extract the annotation data.

But every time that I run my code with a complete file (~2 million variants) I run out of memory. Using indexed files will solve my problem?

[lindenb]

it depends what you what you want to do. Putting everything in memory ? Increasing the memory using xmx could be a solution : http://stackoverflow.com/questions/5374455 if you need to only access a small part of the VCF, yes, indexing (tabix or tribble ) could be a solution.

[dianalemos]

I want to see all the data in the file by accessing small parts of the file each time.