I am trying to find SNPs that are present in one of my samples and absent in the other (controls). I did variant calling with bcftools mpileup and then compare files for respective samples with bcftools isec. I have found some SNPs that should be unique but then when I wanted to confirm that looking on the reads in IGB browser I discovered that many of those SNPs are actually present in my controls as well. I have checked some sites for only one of the samples and I got the same result: there is no change in the .vcf file (so all reads in this position confirm the reference allele), but when I open.bam file in IGB I see the SNP in some of the reads. I did not apply any filters to the variants in .vcf file so any SNP even with low quality should be there. Do you know what can be the cause of this discrepancy? And which data should I trust?
