Analysis of genotype g.vcf
I have a genotype gvcf of 30GB which is causing a RAM issue during analysis. I was wondering if there is a way to get around the size issue and run the genotype gvcf in R or do I need to chunk the gvcf for analysis. Is Python better than R for analysis of bigger gvcf files?
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You perhaps should mention what you want to do with it, in order to get more accurate advice. In general, people will use genotypeGVCFs to make a normal (much smaller) VCF.
I am trying to remove certain elements from the gvcf file, as a preprocessing part for further somatic mutation analysis.
Okay, if you can't be more specific with what you need then I can't help.
In the previous smaller gvcf of individual samples. I expanded the vcf and removed <non-ref> elements from the file, creating a subset of vcf, required for further analysis. I am having trouble loading the genotype gvcf because of huge memory required, thus can't perform the above mentioned steps.
Not sure what you're trying to do - but trying to load a 30Gb into memory in R is never going to work. Much better to use something that streams the file through memory like bcftools.