I am trying to use GATK IndexFeatureFile to create ".vcf.gz.tbi" file. But I have 480 files.
For the pilot study I used:
!./gatk IndexFeatureFile -I HG00096.chrom22.bam.10061.vcf.gz -O HG00096.chrom22.bam.10061.vcf.gz.tbi
Doing this procedure for 480 files is not seem very practical. Is there any way to use all file as an input and it takes all files and gives ".tbi" files as an output?
!./gatk IndexFeatureFile -I *.vcf.gz -O *.vcf.gz.tbi
or maybe not using output argument (just input). I did not worked for me.