I'm trying to use the HaplotypeCaller from the GATK toolkit but I keep getting an error. I pulled GATK through Docker and am using this command:
docker run -v /Users/rimo/ -it broadinstitute/gatk:latest gatk HaplotypeCaller -R /Users/rimo/reference.fasta -I /Users/rimo/sample1.bam -O /Users/rimo/sample1.g.vcf.gz -ERC GVCF
/Users/rimo is my home directory it's where the files are currently located on my computer and it's where I want GATK to look for files to use in the command.
but then I get this error:
A USER ERROR has occurred: The specified fasta file (file:///Users/rimo/reference.fasta) does not exist.
I don't fully understand how Docker commands work but I found a similar problem listed with this issue. I tried to use their solution but it's still giving me the same error as listed above.