gridss2_somatic_sv_call

• This is a snakemake version of gridss2 (https://github.com/PapenfussLab/gridss).

• GRIDSS execution procedures are well described at https://github.com/PapenfussLab/gridss/blob/master/QuickStart.md#optimise-gridss-execution

• After assembly, it performs Normal/Tumor somatic variant calling using gripss. https://github.com/hartwigmedical/hmftools/tree/master/gripss

• GRIDSS being an SV breakpoint caller initially reports all variants as BND but can be post-annotated as Trans, Inv, Ins, Del and Dup with a R script (simple-event-annotation.R). This has already included into snakmakme as last rule rule create_bedpe_with_simpleSVannotation.

• Why all calls BND? https://github.com/PapenfussLab/gridss/blob/master/Readme.md#why-are-all-calls-bnd

• Please specify the samples to be analyzed in config/samples.yaml, following the format explained therein.