Question: Strange variant call it show a indel but looks like a SNP
0
gravatar for cristianrohr768
6.0 years ago by
Spain
cristianrohr76830 wrote:

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?

 

 

 

caller ion variant snp indel • 2.0k views
ADD COMMENTlink modified 18 months ago by Biostar ♦♦ 20 • written 6.0 years ago by cristianrohr76830

What was the variant calling program?

ADD REPLYlink written 6.0 years ago by Manu Prestat4.0k

The torrent variant caller

ADD REPLYlink written 6.0 years ago by cristianrohr76830

This is data from a ION PGM

ADD REPLYlink written 6.0 years ago by cristianrohr76830

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 ?

ADD REPLYlink written 6.0 years ago by Manu Prestat4.0k

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

ADD REPLYlink written 6.0 years ago by cristianrohr76830

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.

ADD REPLYlink written 6.0 years ago by Pierre Lindenbaum130k

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

ADD REPLYlink written 6.0 years ago by cristianrohr76830
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