Strange variant call it show a indel but looks like a SNP

Question

[cristianrohr768]

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:DP: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 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?

[Manu Prestat]

What was the variant calling program?

[cristianrohr768]

The torrent variant caller

[cristianrohr768]

This is data from a ION PGM

[Manu Prestat]

I'm not sure igv would let you visualize insertions... Have you tried with another variant caller (e.g. GATK) to see how consistent is this result ?

[cristianrohr768]

Not yet, I have a typo in the post, now I fix it, you can see that IGV you 5 insertions, they are the blue mark present in five reads, the same that are reported in SAR=5

[Pierre Lindenbaum]

Hello cristianrohr768!

It appears that your post has been cross-posted to another site: http://seqanswers.com/forums/showthread.php?t=47165

This is typically not recommended as it runs the risk of annoying people in both communities.

[cristianrohr768]

I don't know this is not allowed, what i must do? i can't delete the post in seqanswers