Asslamu Alikum

I was generated vcf file from bam and fasta file using gatk tool but when it run on snpeff it shows some warnings and errors in the summary page,

SnpEff version  SnpEff 4.3p (build 2017-06-06 09:55), by Pablo Cingolani
Warnings    1,097,322
Errors  224,360

Is it effect on results and how to solve it?

If any one have a idea about it please help me