Re: [Samtools-help] problem with SNP calling in samtools 0.1.19

[Peter A. <pandolfa@Princeton.EDU>]

The alignment around the site in question can look unremarkable, for example around site 1428, there is:

X_Garnet_Scalloped 1418 . A . 99 . DP=61;QS=1.000000,0.000000,0.000000,0.000000;AF1=0.000;AFE=0.000;DP4=47,14,0,0;MQ=37 PL 0
X_Garnet_Scalloped 1419 . C . 99 . DP=68;QS=1.000000,0.000000,0.000000,0.000000;AF1=0.000;AFE=0.000;DP4=48,20,0,0;MQ=37 PL 0
X_Garnet_Scalloped 1420 . C . 99 . DP=68;QS=1.000000,0.000000,0.000000,0.000000;AF1=0.000;AFE=0.000;DP4=48,20,0,0;MQ=37 PL 0
X_Garnet_Scalloped 1421 . G . 99 . DP=68;QS=1.000000,0.000000,0.000000,0.000000;AF1=0.000;AFE=0.000;DP4=48,20,0,0;MQ=37 PL 0
X_Garnet_Scalloped 1422 . C . 99 . DP=69;QS=1.000000,0.000000,0.000000,0.000000;AF1=0.000;AFE=0.000;DP4=48,21,0,0;MQ=37 PL 0
X_Garnet_Scalloped 1423 . C . 99 . DP=70;QS=1.000000,0.000000,0.000000,0.000000;AF1=0.000;AFE=0.000;DP4=48,22,0,0;MQ=37 PL 0
X_Garnet_Scalloped 1424 . G . 99 . DP=68;QS=1.000000,0.000000,0.000000,0.000000;AF1=0.000;AFE=0.000;DP4=48,20,0,0;MQ=37 PL 0
X_Garnet_Scalloped 1425 . G . 99 . DP=69;QS=1.000000,0.000000,0.000000,0.000000;AF1=0.000;AFE=0.000;DP4=49,20,0,0;MQ=37 PL 0
X_Garnet_Scalloped 1426 . C . 99 . DP=70;QS=1.000000,0.000000,0.000000,0.000000;AF1=0.000;AFE=0.000;DP4=50,20,0,0;MQ=37 PL 0
X_Garnet_Scalloped 1427 . C . 99 . DP=70;QS=1.000000,0.000000,0.000000,0.000000;AF1=0.000;AFE=0.000;DP4=50,20,0,0;MQ=37 PL 0
X_Garnet_Scalloped 1428 . G A 39.1 . DP=67;QS=0.000000,1.000000,0.000000,0.000000;VDB=3.092353e-01;AF1=0.500;AFE=0.500;DP4=0,0,46,19;MQ=37 PL:GT:GQ 255,196,255:0/1:59
X_Garnet_Scalloped 1429 . A . 99 . DP=75;QS=1.000000,0.000000,0.000000,0.000000;AF1=0.000;AFE=0.000;DP4=53,20,0,0;MQ=37 PL 0
X_Garnet_Scalloped 1430 . A . 99 . DP=75;QS=1.000000,0.000000,0.000000,0.000000;AF1=0.000;AFE=0.000;DP4=53,20,0,0;MQ=37 PL 0
X_Garnet_Scalloped 1431 . T . 99 . DP=76;QS=1.000000,0.000000,0.000000,0.000000;AF1=0.000;AFE=0.000;DP4=55,21,0,0;MQ=37 PL 0
X_Garnet_Scalloped 1432 . C . 99 . DP=80;QS=1.000000,0.000000,0.000000,0.000000;AF1=0.000;AFE=0.000;DP4=55,25,0,0;MQ=37 PL 0
X_Garnet_Scalloped 1433 . C . 99 . DP=79;QS=1.000000,0.000000,0.000000,0.000000;AF1=0.000;AFE=0.000;DP4=54,25,0,0;MQ=37 PL 0
X_Garnet_Scalloped 1434 . G . 99 . DP=76;QS=0.986455,0.013545,0.000000,0.000000;RPB=1.048437e+00;AF1=0.000;AFE=0.000;DP4=51,24,1,0;MQ=37;PV4=1,1,1,1 PL 0
X_Garnet_Scalloped 1435 . C . 99 . DP=80;QS=1.000000,0.000000,0.000000,0.000000;AF1=0.000;AFE=0.000;DP4=55,25,0,0;MQ=37 PL 0
X_Garnet_Scalloped 1436 . C . 99 . DP=86;QS=1.000000,0.000000,0.000000,0.000000;AF1=0.000;AFE=0.000;DP4=60,26,0,0;MQ=37 PL 0
X_Garnet_Scalloped 1437 . G . 99 . DP=86;QS=1.000000,0.000000,0.000000,0.000000;AF1=0.000;AFE=0.000;DP4=60,26,0,0;MQ=37 PL 0
X_Garnet_Scalloped 1438 . G . 99 . DP=86;QS=1.000000,0.000000,0.000000,0.000000;AF1=0.000;AFE=0.000;DP4=60,26,0,0;MQ=37 PL 0

I will have to check the bam to see if the DP4 reporting or the genotype call is the error.

Peter

_____________________
Peter Andolfatto
Associate Professor
Princeton University



On Mar 20, 2014, at 12:19 PM, David Garfield <dav...@em...<mailto:dav...@em...>> wrote:

I wish I had a solution for you, but I'm similarly boggled by a lack of understanding as to what exactly these new INFO fields are.

With respect to the original problem, what does the mpileup output look like for those regions? Is the issue with the genotype call or in the reporting for the DP reporting itself?

Best wishes,

David


-------------------------------------------------------------------------------------
David Garfield, PhD
Furlong Group
European Molecular Biology Laboratory (EMBL)

Telephone    +49 6221 387 8426
Fax                 +49 6221 387 166
E-mail dav...@em...<mailto:dav...@em...>
Snail Meyerhofstraße 1
D-69012 Heidelberg
Germany