Hey guys, im trying to merge multiple vcf files with the Genome Analysis Toolkit (V. 3.5). Usually when dealing with few samples the command would be something like this:
java -jar GenomeAnalysisTK.jar -T CombineVariants -R ../reference.fa --variant sample1.vcf --variant sample2.vcf --variant sample3.vcf --variant sample4.vcf --variant sample5.vcf --variant sample6.vcf -o merge_file.vcf
The problem I have right now is I have many vcf files I want to merge (not just 6 like in the previous example). I have been digging through the command [options] but there is no option to select for example a whole directory with the vcf's in it. Or alternatively write something like ''--variant *.vcf'' so that it selects all of my vcf files and applies the CombineVariants to them.
So in conclusion my question is this: Is typing one by one the vcf files the only way of running this command with many vcfs?