The current GATK version is 3.6-0
Examples: Monday, today, last week, Mar 26, 3/26/04

Howdy, Stranger!

It looks like you're new here. If you want to get involved, click one of these buttons!

Powered by Vanilla. Made with Bootstrap.

Why SNP not called in one sample

awitneyawitney Member Posts: 3
edited January 2013 in Ask the GATK team


I am fairly new to GATK, but am trying to call SNPs in two bacterial strains against a single reference. In one strain the SNP is called, but not the other... looking at the alignment in IGV and also all sites (-out_mode EMIT_ALL_SITES) I can't understand why the SNP was not called in the second strain.

For the first strain, for which GATK calls the SNP
NC_011770 9650 . C T 645.75 PASS AC=2;AF=1.00;AN=2;BaseQRankSum=-2.149;DP=43;Dels=0.05;FS=4.191;HRun=2;HaplotypeScore=5.6633;MQ=64.95;MQ0=0;MQRankSum=0.878;QD=15.02;ReadPosRankSum=2.270;SB=-255.73 GT:AD:DP:GQ:PL 1/1:2,39:41:46.50:679,46,0

For the second strain, for which GATK does NOT call the SNP:
NC_011770 9650 . C T 942.90 PASS AC=2;AF=1.00;AN=2;DP=53;Dels=0.06;FS=0.000;HRun=2;HaplotypeScore=23.7546;MQ=53.63;MQ0=0;QD=17.79;SB=-393.80 GT:AD:DP:GQ:PL 1/1:0,47:50:99:976,105,0

UnifiedGenotyper was called with these options:

-stand_call_conf 30.0 -stand_emit_conf 10.0 -dcov 100 -out_mode EMIT_ALL_SITES

Does anyone know why GATK does not call a SNP in the second strain?

Thanks for any help


Post edited by Geraldine_VdAuwera on


Sign In or Register to comment.