Same statistical results from different snpeff runnings.

[Khewahah]

Describe the issue
I got very similar even same results(.html) after running snpeff with several population vcf files which are seperated from a total vcf file.

To Reproduce

1. SnpEff version: V5.1
2. Genome version: assembled by ourselves
3. SnpEff full command line:
   java -jar snpEff.jar build -gff3 -v genome.ver.2.0.0 -config ~/softwares/snpEff-5.1/snpEff.config
   java -Xmx8g -Dsnpeff.parallel.threads=64 -jar snpEff.jar -v -canon genome.ver.2.0.0 -stats temp1.indel.html temp1.indel.vcf.gz | bgzip > anno_temp1.indel.vcf.gz
4. Output:
   
   
   
   i'm not sure whether you can see these pics, but they(html files) are totally same.
   And this is the seperation command:
   bcftools view --threads 64 -S sample.list --force-samples merged.indel.vcf.gz | bgzip > temp1.snp.vcf.gz

Expected behavior
So, I need you tell me what to do to get real annotation of different samples.