By using BWA and GATK, I have made a vcf file of my raw SNPs. Then I filtered that and kept just homozygous SNPs in my new vcf file with all the header information. Then I compressed and indexed my vcf file and trying to read the vcf.gz file on Artemis but it's not reading my new filtered vcf.gz file though still it can read my raw vcf.gz file.
The SNP and INDEL files I produced using GATK was error-free but during compressing and indexing steps I did the mistake. The VCF files need to be compressed and indexed using bgzip and tabix as below:
bgzip file.vcf (will create file.vcf.gz) tabix -p vcf file.vcf.gz (will create file.vcf.gz.tbi)
I didn't use the (-p vcf) flag so it didn't work on artemis as it didn't recognize the vcf file. I had a chat with the author of Artemis Tim Carver who guided me all the way. Thanks Tim.