Zygosity from SRA reads

[jimsac2016]

I'm presently confused into how to determine whether a particular SNP (as shown by alignment of a reference mammalian genome to an SRA on the NCBI sequence viewer) is homozygous or heterozygous. I notice that for some SNPs about half the SRA reads correspond to one allele and the other half show the other allele. I'm assuming this is heterozygous, as opposed to when, at the same position only one allele appears or perhaps it appears in 9 out of 10 alignments. Am I correct here?
Thanks for any insight you may be able to provide!

[dpryan]

I wouldn't recommend trying to visually call variants with NGS data. Run your BAM files through a variant caller (samtools mpileup, GATK, etc.) and just look at the VCF file.

[jimsac2016]

Zygosity

Thanks for the suggestion, dpryan. Will need to figure this out!