Reducing filesize for homozygosity mapper

Question

[lisa science]

Dear all,

I wanted the homozygosity mapper tool for finding homozygous regions in two affected individuals in a family of four. The data can only be entered in a combined vcf for which the original bam files need to be used. the command mentioned for the purpose is

samtools mpileup -D -gf /path/to/genome.fa *.bam | bcftools view -c -g - > filename.vcf 

I have four bam files (~3-4GB) which generate a combined vcf of 8 GB which cannot be uploaded. Any suggestions?

Thanks :)