I'm doing some analysis and I need to subset a large VCF file (~8GB gziped) given a bed interval and identify within a subset of rsid.
Unfortunately, both my normal choices to do this analysis (
bedtools) are taking way to long or failing due to memory issues in my local computer and a remote server.
Do you guys know any other options or suggestions to speed up this process?
Follow the commands I use:
bedtools intersect -a <myvcf>.vcf.gz -b <myinterval>.bed -wa | \ java -Xmx10g -jar snpSift.jar filter --set <myrsid>.txt "ID in SET"
gzcat <myvcf>.vcf.gz | \ java -Xmx10g -jar snpSift.jar intervals <mybed>.bed | \ java -Xmx10g -jar snpSift.jar filter --set <myrsid>.txt "ID in SET"
bedtools command usually fail due to unknown reason and
SnpSift runs over 6 hours even given 10GB of ram. My local machine have 8GB of RAM, but the server have 32GB.