GATK v18.104.22.168 HaplotypeCaller
I am using GATK v22.214.171.124 HaplotypeCaller for variant analysis. (paired-end DNA sequenced data mapped to the reference using BWA mem).
The command I used;
“gatk HaplotypeCaller –R Reference.fna –I input.bam –O output.vcf”
It runs for a while (couple of seconds) but does not produce an output. No error message was given. Am I doing this right? Any help is appreciated.