I am using parabrick for my wes data. After somatic variant calling, I am trying to annotate variants using dbsnp database (if there are any known germline variants present by chance) with pbrun dbsnp module but I am not getting either any error or warning. Initially, I thought there might be an issue with either vcf file or dbsnp file so I generated vcf file again and downloaded the dbsnp database vcf file again and generated their tabix index. And I also tried with Gnomd database germline resources which also contains the rsids. In both the caes it shows only -1 which is not clear to me. Here is the screenshot of the command and its response. Kindly suggest.
Hi,
Thanks for your interest in Parabricks. Seems the run completed but the progress meter didn’t catch up fast enough. Do you get an output and is it as expected ?