Strange variant call it show a indel but looks like a SNP
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7.1 years ago

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 the alignment in IGV i see the following

http://i57.tinypic.com/sdpqme.jpg

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?

 

 

 

ion variant SNP indel caller • 2.3k views
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What was the variant calling program?

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The torrent variant caller

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This is data from a ION PGM

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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 ?

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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

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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.

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

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