Hello everyone,

I'm a novice in bioinformatics and trying to call variants form SARS-CoV-2 genome using GATK HaplotypeCaller version 4.2.4.1 in conda environment within WSL2.

$ gatk HaplotypeCaller -R reference-genome-sars-cov-2.fasta -I SRA_final.bam -O SRA.vcf

and when I checked the .vcf file, it's empty. I know that gatk HaplotypeCaller will automatically filter several parameters so I added the -DF (disable-read-filter) arguments as below:

$ gatk HaplotypeCaller -R reference-genome-sars-cov-2.fasta -I SRA_final.bam -O SRA.vcf -DF MappingQualityAvailableReadFilter MappingQualityReadFilter

but returned an error:

A USER ERROR has occurred: Illegal argument value: Positional arguments were provided ',MappingQualityReadFilter}' but no positional argument is defined for this tool.

I'm baffled as to what value should I add to the arguments. I'm aware that gatk set the default mapping quality value threshold at 20. Given that I used bbduk in the previous trimming and bbduk calculates the average quality score in a different way than other trimmers, I'd like to lower the quality score cut-off.

Any inputs will be highly appreciated. Thanks.