I have a variant from a ION PGM sequencing, called with the ION Torrent variant caller plugin
CHR POS ID REF ALT chr22 44324726 . T TG
The flow cell evaluator say this is a insertion
FSAF = 16,
FSAR = 11,
FSRF = 0,
FSRR = 0, but the observations are
SAF = 0,
If I look at the alignment in IGV I see the following
I check in dbSNP and in the position 44324727 a well known C/G snp 1KG MAF G=0.284 rs738409
and the T variant at position 44324730 is also known rs738408
So in my opinion is more likely a C/G rs738409 SNP, than a novel insertion, and even more it looks like a strand bias because the observed alternate allele as an insertion is only in the reverse strand.
What's your opinion?