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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