I am currently testing different variant callers on my sample (NA12878) and the majority of other variant callers generate 30,000 variants in this sample, while freebayes returned 300,000 which is strange. I filtered all variants with QUAL = 0 and there were still over 90,000 variants. I am looking for recommendations on how to run freebyes on WES samples.

The command I used:

freebayes -f /primary_assembly_hg38.fa -t Twist_Exome_Target_hg38.bed Coriell.bam > FB.vcf