Hello,
I would like to push your attention to a problem which I allready reported at the freebayes git repository.
In my reference sequence there is a pattern 11 times TG followed by 7 times T. Now I have a sample which I already sequenced by sanger resulting in one allel with 11xTG/5xT and one with 12xTG/7xT.
If I have a look at the alignment file for my NGS analysis I can guess the same result. But freebayes says there are 11/12xTG (which is ok) and a SNP T>G which is not the same as a 2bp deletion. In contrast gatk's HaplotypeCaller have the correct result.
I don't understand what freebayes is doing here. Are there any parameters with which I can influence the result.
On freebayes git site you can see the relevant position in igv. What more information can I provide to you?
Thanks a lot.
fin swimmer
I would like to push your attention to a problem which I allready reported at the freebayes git repository.
In my reference sequence there is a pattern 11 times TG followed by 7 times T. Now I have a sample which I already sequenced by sanger resulting in one allel with 11xTG/5xT and one with 12xTG/7xT.
If I have a look at the alignment file for my NGS analysis I can guess the same result. But freebayes says there are 11/12xTG (which is ok) and a SNP T>G which is not the same as a 2bp deletion. In contrast gatk's HaplotypeCaller have the correct result.
I don't understand what freebayes is doing here. Are there any parameters with which I can influence the result.
On freebayes git site you can see the relevant position in igv. What more information can I provide to you?
Thanks a lot.
fin swimmer
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