HELP: haplotypecaller doesn't call the driver oncogenic variant!
I'm using GATK haplotypecaller in order to detect varianti in a tumor sample analyzed with Illumina WES 100X2 paired end mode. I know KRAS p.G12 variant (chr12:25398284) is present in my sample (because previously seen with Sanger sequencing, KRAS is the oncogenic event in this kind of tumor). I aligned the fastq file with bwa after quality control e adapter trimmig. In my bam file I'm able to view the variant at genomic coordinate chr12:25398284 as you can see in the picture (IGV):
however GATK haplotypecaller doesn't call the variant anyway.
This is my basic command line:
java -Xmx4g -jar /opt/GenomeAnalysisTK-3.3-0/GenomeAnalysisTK.jar -T HaplotypeCaller -R human_g1k_v37.fasta -I my.bam -stand_call_conf 0 -stand_emit_conf 0 -o output.file
and I tryed to tune a a lot of parameter such as stand_call_conf; -stand_emit_conf; --heterozygosity; --min_base_quality_score and so on.
The base quality is good and the mapping quality too, but the haplotypecaller does not determine any active region around the position
Any suggestion about the reason of misscalling??