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SNV variant not identified with haplotype caller
I used haplotype caller on 3 bam files, producing gvcf and one groupe vcf afterwards. IGV show 2 HET and one REF.
But GATK gave me 1REF,1HET,1REF. The coverage at this position is around 100 with 50% variants. The only otions used for the calling are -L and -D. The bam have been preprocessed with GATK for duplicates and recalibration.
Freebayes give me the right genotypes !!!
I tried GATK 3.7, 4.0 and 4.1. I also tried on the raw bam and before recalibration. Still the same.
When I do a group calling without individual gvcf output, this variant completely disapear ???
I am stuck on this since I don't really know how to investigate further?
What should I do to figure out why this specific variant does not seems to be identified by haplotype caller.