Hi,

Is there a way to force GATK haplotypecaller to output all genomic positions in the vcf; not only variant ones ?

Example here :

Top : Raw bam file 

Middle : -outbam using : `gatk HaplotypeCaller -R $genome -O test.vcf -I in.bam -ERC GVCF --max-alternate-alleles 3  -bamout test.bam -L interval.bed --output-mode EMIT_ALL_ACTIVE_SITES`

bottom : -outbam using `gatk HaplotypeCaller -R $genome -O test.vcf -I in.bam -ERC GVCF --max-alternate-alleles 3  -bamout test.bam -L interval.bed --output-mode EMIT_ALL_CONFIDENT_SITES`

You can see that the region without variant sites are not processed by haplotypecaller ; even with EMIT_ALL_ACTIVE_SITES and EMIT_ALL_CONFIDENT SITES.

Any idea how to tune haplotypecaller to output all sites with enough coverage ?

gatk version : 4.1.7.0

![enter image description here][1]


  [1]: https://i.ibb.co/Dtk8WwK/igv.png


Thanks
`gatk HaplotypeCaller -R {reference} -I {bam_path} -L {bed_path} -ERC BP_RESOLUTION -O {out_vcf}`

Maybe look at BP_RESOLUTION