So many homozygote variants in vcf

Question

[mary99]

Dear all, Recently I've got several vcf files from ion torent seuencer.I supposed to do filtering and reporting most probable gene(s).My problem is that most Genotype are reported as variant homozygote (1/1 ) with good numbers of suporting reads.Unfortunatly i dont have MQ field in vcf files.I tried by filtering another fields to get rid of false positive variants but at the end since most of GT are homozygote, it is hard to decide.Plus that I don't have the bam files.I think may be those reads which support variants don't have good quality for mapping!Does any one have had such experince?How i can conclude about this data? Thanks in advance

[Kevin Blighe]

I have only seen this when read-depth was low, but you report that it is high. Do you have any other stats or information for your samples, like:

• DNA extraction protocol
• Animal species (Human?)
• Alignment metrics
• Analysis method (presumably Torrent Suite)