Question: bcftools call transforms the mpileup -3aag variant into a TAAGAAGA>TAAGA variant
0
gravatar for Michi
4.1 years ago by
Michi950
Barcelona
Michi950 wrote:

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 reperesentation given above..

 

 

 

ADD COMMENTlink modified 4.1 years ago • written 4.1 years ago by Michi950
2
gravatar for Devon Ryan
4.1 years ago by
Devon Ryan93k
Freiburg, Germany
Devon Ryan93k wrote:

The outputs are in complete agreement, they both say that AAG is deleted, they just represent that in different ways.

ADD COMMENTlink written 4.1 years ago by Devon Ryan93k

Ha, I was really hoping that was the answer, but I cannot see it.

If you remove TAAGA from TAAGAAGA, the result is AGA as a difference, ergo the deletion.. Now I assume I am wrong with my argument, so could you please elaborate? Thank you

ADD REPLYlink modified 20 days ago by RamRS25k • written 4.1 years ago by Michi950
1

TAAGA isn't what's removed, it's the result of the change (i.e., we start with TAAGAAGA, something happens, and we then see TAAGA). VCF files will represent the states observed, not a reference and then change.

ADD REPLYlink written 4.1 years ago by Devon Ryan93k
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