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GATK188.8.131.52 HaplotypeCaller called wrong variant
I got a strange issue. I was looking for EGFR C797S in my sample using gatk 184.108.40.206 HaplotypeCaller. But instead HaplotypeCaller reported C797G:
chr7 55249091 COSM6493936 T G 9228.6 . AC=1;AF=0.500;AN=2;ANN=G|missense_variant|MODERATE|EGFR|EGFR|transcript|NM_005228.3|protein_coding|20/28|c.2389T>G|p.Cys797Gly|2635/5600|2389/3633|797/1210||;BaseQRankSum=-8.760e-01;DP=11630;ExcessHet=3.0103;FS=119.585;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.856;QD=1.33;ReadPosRankSum=20.47;SOR=8.736;AA=p.C797G;CDS=c.2389T>G;CNT=1;GENE=EGFR;STRAND=+ GT:AD:DP:GQ:PL 0/1:6078,878:8673:99:9236,0,203073
But from the bam file before HaplotypeCaller and the bam output from HaplotypeCaller all show the alt is A in igv, not the G called by HaplotypeCaller. The software coming with the sequencer called C797S correctly.
I used the all default settings except "--max-reads-per-alignment-start 0 --disable-read-filter NotDuplicateReadFilter" to run HaplotypeCaller because we work with amplicon-based data.
Thanks a lot for the help!