The frontline support team will be slow on the forum because we are occupied with the GATK Workshop on March 21st and 22nd 2019. We will be back and more available to answer questions on the forum on March 25th 2019.
GATK v126.96.36.199 HaplotypeCaller
I am using GATK v188.8.131.52 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.