I have a VCF file that has 35718025 positions/loci. I am trying to add more accessions (let's say accession1, accession2, and accession3) into this VCF using
bcftools merge. When I perform haplotype calling using the GATK HaplotypeCaller, how can I output exact 35718025 positions/loci for the accession1, accession2, and accession3?
I have tried using
GATK HaplotypeCaller --force-call-filtered-alleles --alleles <the VCF file that has 35718025 loci>, but the output VCF files have more than 35718025 positions/loci. Does anybody have any suggestions for me to solve this problem?