INDEL calls instead of SNVs at neigboring loci

[axelgschwind]

Dear Illumina team,

I have a tumor-normal pair in which something weird happened. The tumor sample has two SNVs in BRAF at loci next to each other: chr7:140453136A>C chr7:140453137C>T In the normal sample, there are no SNPs at these loci.

When I run the latest strelka2 version (2.9.10), however, it does not call these variants. Instead, it calls two one-base-indels and one SNV:

chr7:140453134TC>T chr7:140453136A>C chr7:140453137C>CT

Is there maybe something wrong with my settings? However, I remember that it happend at some point for another sample. I have extracted the corresponding region of the BAM files and uploaded these files here: https://cloud.imgag.de/index.php/s/eFzwntRzd9i5Z8a (normal sample) https://cloud.imgag.de/index.php/s/23GWWKTRLbPpQGH (tumor sample)

It would be great if you could give me a hint about what went wrong.

best,

Axel