I received (from manufacturer) several .bam files and I used four callers (samtools, freebayes, haplotypecaller, deepvariant) to find some sequence variants. In obtained .vcf files, I took a closer look to some calls. I found interesting, homozygous one rs477033 (C/G Ref/Alt) with flag 'COMMON=0' and very low MAF. I also checked the .bam file (in IGV) and this rs itself in ensembl database. It looks like this:
The problem is: in this case ref and alt are switched. The G is reference (ancestral) allele and C is altered. Nevertheless in the .bam file it's interpreted in opposite way. Of course it's false positive variant - there's no mutation there at all. All variant callers returned it as high quality variant. My. bam files are full of them.
What went wrong in this case? Problem with mapping?
How can I fix this thing, to get only novel and rare true positive variants?