Question: I have a number of phased variant calls in a Long Ranger VCF. Some of these calls have a HAPLOTYPECALLED=1 while others have a HAPLOTYPECALLED=0 in the info field. What is the HAPLOCALLED Info field?
Answer: Long Ranger calls SNVs and small indels with GATK or FreeBayes. After initial variant calling and phasing, the variant caller is invoked separately in 'haploid mode' on reads from each phased haplotype. This step boosts the sensitivity of the variant calls by calling low-allele fraction variants that are the dominant allele on one haplotype. Variants called in this phase will be tagged with HAPLOCALLED=1 in the INFO field.
For more information please see the Phased VCF page.