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Thanks @shlee I will try out the suggestions made by you. Lets see if what can make this work :)
(Quote) As posted originally my command was : nohup java -jar /dummy/GenomeAnalysisTK-3.7-0-gcfedb67/GenomeAnalysisTK.jar -T SelectVariants --variant Calling.vcf -R REF.fasta -o Biallelic.vcf -restrictAllelesTo BIALLELIC & and it can be seen -…
(Quote) i have been able to achieve this by a using a different tool. However when I use SelectVariants to split the merged vcf file (with 10 samples) into sample wise vcf its showing the run time to be 1500 weeks or so. The process even starts off …
(Quote) All most all the utilities are slow not just a few. Its really troubling me as to what may be going wrong. There is sufficient RAM space as well.
(Quote) Even with Java 1.8 it is slow.
I was having a "ERROR StatusLogger Log4j2 could not find a logging implementation" error and I tried to rectify it with the nighly build but with no avail The version of nightly build is : GenomeAnalysisTK-nightly-2017-12-11-1 The version…