Hi, from a previous run of my sample, I know that at the position in question there is a TAAG>T variant (deletion of AAG), which is also clearly visible in IGV.

A samtools mpileup confirms this:

1    225685621    T    10    ,,,-3aag,-3aag,-3aag,-3aag,,-3aag,,-3aag    CFFG7GGWGG    34    <<<<<<<>>><<<<<><>><>>>><<><<<>>><    CFHHJJJHFIIEJJGJJJJJJIJJJFCFFEJJHD

But, and here is my issue, the bcftoolsc call, or bcftools view command turns this variant into the following, which disagrees with the previous outputs

1    225685621    .    TAAGAAGA    TAAGA    174    .    INDEL;IDV=7;IMF=0.636364;DP=11;VDB=0.0633369;SGB=-0.616816;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=0,2,0,6;MQ=60    GT:PL:DP:DV:DP4    0/1:208,0,87:8:6:0,2,0,6

Thus, I'd like to understand why this is happening, and how I could prevent that behaviour. Is it possible that this is a bug?

Thanks for any help,
Michael

EDIT:

I could solve the problem by normalizing the call with piping the bcftools call output to:

bcftools norm -f genome.fa -

But still, I do not understand the representation given above.