Variant calling using HaplotypeCaller does not show #FILTER information

Question

[QX]

Hi All,

I would like to ask for Variant Calling using HaplotypeCaller. It's supposed that after doing the HaplotypeCaller, the #FILTER columns in gvcf files shall show the 'PASS/LowQ' however in my case, the output #FILTER only shows '.' without any rows showing 'PASS' or not:

ref_gene=Homo_sapiens.GRCh38.dna.primary_assembly_ERCC.fa
input=$1 #BQSR.bam file
output=`echo "${input%%.*}"`.gvcf.gz

This is the code:

$path_gatk HaplotypeCaller -R $ref_gene -I $input -O $output -ERC GVCF --dragen-mode true

[Pierre Lindenbaum]

It's supposed that after doing the HaplotypeCaller, the #FILTER columns in gvcf files shall show the 'PASS/LowQ'

where did you find such assertion ? such FILTER is set after something like VariantFiltration https://gatk.broadinstitute.org/hc/en-us/articles/360037434691-VariantFiltration . Furthermore, you're running HC in GVCF mode, I wouldn't expect a FILTER at this step.