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,
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 reperesentation given above..