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# Why SNP not called in one sample

Member
edited January 2013

Hi,

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

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
Tagged:

• Member
edited July 2012

Thanks for that Phil. No I had not found that link before, but very helpful indeed. On closer inspection in IGV it looks like the extra deletions are probably homopolymer problems (This is Ion Torrent data), but now I know what to look for!

Thanks again