get_mut_type for indels results in empty GRangesList

UMCUGenetics / MutationalPatterns

R package for extracting and visualizing mutational patterns in base substitution catalogues

MIT License

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get_mut_type for indels results in empty GRangesList #72

Closed kristianunger closed 2 years ago

kristianunger commented 2 years ago

Hi there,

when I try to get get indels using the get_mut_type function from a Mutect2 (tumor/normal pairs) vcf (mouse) I get an empty granges objects although there should be indels by manually inspecting the vcf. SNVs load fine and DBS also is empty. The reference genome I was using for Mutect2 analysis was GRCm38.p6 which should be fine with BSgenome.Mmusculus.UCSC.mm10. Can you give me direction what could go wrong?

Many thanks,

Kristian

FreekManders commented 2 years ago

Hi Kristian,

The read_vcfs_as_granges function by default only reads the SNVs. Did you set it to type = "all" to include all variants? Additionally, what version of the package are you using?

kristianunger commented 2 years ago

Thank you! I am using the latest BioC version.

Adding type = "all" did the trick.

I followed the docu https://bioconductor.org/packages/release/bioc/vignettes/MutationalPatterns/inst/doc/Introduction_to_MutationalPatterns.html#load-example-data-indels-dbss-and-mbss and used the function as described for loading SNVs only.