I am running the following command on gVCF files of 70 samples (s1-s70) to get joint VCF file:
java -Xmx2g -jar GenomeAnalysisTK.jar -R ucsc.hg19.fasta
-T GenotypeGVCFs --variant s1.vcf --variant S70.vcf
-o all.vcf > joint.out
It runs for 4 days already and it is just on the 10 chr. Anyone has suggestion how to speed things up, or this always the process?
Thank you for your help,