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This is a snakemake version of gridss2 (https://github.com/PapenfussLab/gridss).
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GRIDSS execution procedures are well described at https://github.com/PapenfussLab/gridss/blob/master/QuickStart.md#optimise-gridss-execution
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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
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Please specify the samples to be analyzed in config/samples.yaml, following the format explained therein.