I've been using samtools/GATK to call for SNP/indels these days, and would like to filter my data against known common variants, to achieve rare events.
Some of the samtools results can be:
#CHROM POS ID REF ALT 1 10177 . ACCT ACCCT
There could be several alternatives for both REF and ALT sequence. So when I compare my SNP/indel with common SNP database; should I just compare the position using bedtools, or should I look into the change of bases? For example, if in database, on position 1, it's a SNP changing from G to C; while my results indicate also at position 1,but changing from G to T. Then should I regard this as common SNP or rare SNP?