I just created a vcf file for multiple genomes using the following command below, but it generates vcf4.2 version. I am using a tool that only accepts 4.1 version. Is there a way to downgrade a vcf file to 4.1. Also, what options do I need to change to create vcf4.1 in GATK?
java -Xmx58g -Djava.io.tmpdir=$SCRATCH -jar $GATK/GenomeAnalysisTK.jar \ -R $GENOME/UCSC_ALL_FULL_CHROMS_HG19.fasta \ -nt 10 \ -T UnifiedGenotyper \