a) GATK v4.3.0.0

b) Exact command used: Bash pipeline locally created be me to run WES

# Dragen Haplotypecaller Functional Equivalent

${GATK} HaplotypeCaller \
-R ${ref} \
-I ${after-DRAGEN-STR-Model-bam" \
-L ${interval-bed}
-ip 150 \
-O "dragen-FunctionalEquivalent.vcf.gz \
-GQB 10 -GQB 20 -GQB 30 -GQB 40 -GQB 50 -GQB 60 -GQB 70 -GQB 80 -GQB 90 \
--dragen-mode true \
--dragstr-params-path dragstr_model.txt \
--disable-spanning-event-genotyping true \
--tmp-dir tmp

c) Entire program log:

Hi, is the first time I use Dragen ... when I go to check the VCF I see several zygosities

N. of Variant --- Zygosity

   7487 --- 0/0
 35524 --- 0/1
        1  --- 0/2
 32643 --- 1/1
     336 --- 1/2
         1 --- 1/3
       17 --- 2/2

Why do I have 0/0 in my VCF? They use to have a very low coverage, as also the alternative allele a coverage around 1-3. Is there any option to add in my above code to to avoid those calls?

In case I can exclude downstream the 0/0 with:

${GATK} SelectVariants -R ${REF} -V dragen.vcf.gz --exclude-non-variants true -O output.vcf

How can I avoid calls 1/2, 1/3, 2/2 ? ... I can not validate the VCF with these calls

${GATK} ValidateVariants -R ${REF} -V input.vcf

Thank you for the help!