Dear All,

I am running GATK4 via docker to run HaplotypeCaller in my Mac OS terminal.

I have connected the docker to my files as follows

$  docker run -v /Users/imac/Documents/NA12878/myproject:/gatk/myfile -it broadinstitute/gatk:4.1.3.0

then run the Haplotype caller via the gatk in the docker.

(gatk) myfile # HaplotypeCaller -R ref.fa -I file1_mrkdup.bam -O file1_variant2.vcf

However when I leave the system, the docker container disconnects. Any help will be appreciated.

Do we have an alternative version of caffeinate in docker?

Any help would be appreciated.

Thanks
Smeeta