Losing ~60% of variants from sequence data after phasing with SHAPEIT

I have a sequenced locus on chromosome 9 that I am attempting to phase with SHAPEIT. My original vcf file has1617 variants. After phasing with SHAPEIT I am left with only 513 variants. I made sure to check the quality of my vcf with checkVCF and found no duplicates or reference mismatches.

I use the following code to run SHAPEIT:

shapeit4.2 –input my_data.vcf.gz –map chr9.b37.gmap.gz –region 9
–reference 1000g_phase3_nomulti_allelic/ALL.chr9.phase3_shapeit2_mvncall_integrated_v5b.20130502.genotypes.vcf.gz
–thread 8 –log shapeit_chr9.log –output my_data_phased_SHAPEIT.vcf –mcmc-iterations 10b,1p,1b,1p,1b,1p,1b,1p,10m –pbwt-depth 8 &

Is there a way to minimize the loss of variants?