I'm using annovar to filter common variants using different database, in order to find rare variants. Then I pay special attention to the allele frequency of alternative alleles.
Here is an example of same SNP from both dbsnp and 1000Genome Project:
1 1282270 rs307356 T C . PASS G5;GCF;GENEINFO=DVL1:1855;GMAF=0.0406764168190128;GNO;KGPilot123;RSPOS=1282270;SAO=0;SLO;SSR=0;VC=SNV;VLD;VP=050100000000050110000101;WGT=0;dbSNPBuildID=79
From 1000G (I would say, annovar format converted from 1000G):
1 1282270 T C 0.96 rs307356
From this example, I then realized my long-time confusion between "minor allele frequency" and "alternative allele frequency". This seems to me that, reference allele T is minor; while alternative C is major here.
I used to think "alternative allele" is "minor allele", and now seems it's wrong. Then regardless of minor/major, can I infer what is alternative allele frequency from the above vcf files? thx