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Hello all,
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
GT:AO
P:FAO:FDP:FRO:FSAF:FSAR:FSRF:FSRR:GQ:RO:SAF:SAR:SRF:SRR
1/1:5:27:27:27:0:16:11:0:0:11:22:0:5:16:6
You see FSAF = 16, FSAR = 11, FSRF = 0, FSRR = 0, but the observations are
SAF = 0, SAR=5, SRF=16, SRR=6
if i look 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 you opinion?
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
GT:AO
P:FAO:FDP:FRO:FSAF:FSAR:FSRF:FSRR:GQ:RO:SAF:SAR:SRF:SRR1/1:5:27:27:27:0:16:11:0:0:11:22:0:5:16:6
You see FSAF = 16, FSAR = 11, FSRF = 0, FSRR = 0, but the observations are
SAF = 0, SAR=5, SRF=16, SRR=6
if i look 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 you opinion?
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