How to merge multiple patient's vcf files (indel and snv) with different IDs?

Question

[Zahra]

Hi all, I have some VCF files for my patients, each patient has 2 files( indel.vcf , snv.vcf) and I want to merge these file by the script bellow:

java -jar gatk-package-4.2.0.0-local.jar  MergeVcfs -I /PATH_TO_patient1_ID_indel.vcf  -I /PATH_TO_patient1_ID_snv.vcf -O /PATH_TO_patient1_ID_merged.vcf

I don't know how to do this for multiple patients with different IDs.

Thanks for any help.

[German.M.Demidov]

bcftools concat may help