I need suggestions in creating index and dictionary with vcf files. For the base recalibration step, I downloaded Homo_sapiens_assembly38.known_indels.vcf.gz from the given link: https://console.cloud.google.com/storage/browser/genomics-public-data/resources/broad/hg38/v0;tab=objects?prefix=&forceOnObjectsSortingFiltering=false
I am using GATK version 18.104.22.168
When I try to create index and dictoionary of the vcf file, I get the following error: no suitable codecs found. I also tried to check the vcf file using ValidateVariants and I get the same error: no suitable codecs found.
Can anyone suggest which indels vcf file is used for masking sites in the base recalibration step. Has anyone come across this above error and how did they resolve the issue.