Axel Gschwind

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...

Hello, we are using svtools to creating bedpe files that originate both from MANTA and Delly. In some cases, MANTA generates a structural variant call that looks like this: `chrX...

hla-genotyper will be benchmarked and compared to OptiType. If successful, we need to caclulate the HLA genotypes for our somatic cohort and we will compare it to the european distribution...

- gene definition as overlap of ensembl transcripts - flag partially affected genes - implement also for structural variants (DEL, INV and DUP)

Include SVs into somatic report configuration.

1

Currently, somatic structural variants are chosen by hand. Like germline SVs, somatic SVs should be imported into NGSD and the user should be able to select a SV for the...

The options for exclusion from report "low tumor content", "low copy number" and "high BAF deviation" have not been used yet. Add option "not protein-altering" and "repeat region". No change...