# Dictionary and index of vcf for base recalibration step

I am using GATK version 4.2.2.0

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.

Thanks

• Can you show which commands are you trying on the file? Oct 2 '21 at 14:53

• Additionally, you may want to just use the less command to look inside the file and see if anything appears to be corrupted (you may need to decompress it for that purpose).
• It may also be worth trying to gunzip or gzip -d commands to decompress the file (assuming you have the drive space). This will both ensure that decompressing the file on the fly is not causing any grief to GATK (which is unlikely) and that the file decompresses without error (which would also be an indication of corruption).