Calling for one specific SNP from multiple sequencing runs
Getting SNPs from whole-genome data is usually done via mapping sequencing reads on the reference (bwa-mem or bowtie are two popular mappers) and then using one of variant calling tools (like freebayes, samtools, or GATK). However, I would also look up if there is something virus-specific.
According to this answer, you could get variant calls of a specific region using samtools if you give it a bed file that contains the region of interest (three columns chr    start    stop format). For example using human reference
samtools mpileup -uDl regions.bed -f hg19.fa file1.sorted.bam file2.sorted.bam | bcftools view -bvcg - &gt; RAL_samtools.raw.bcf

You could also specify a bunch of files, not just two and it would do the variant calling on them all.